Probably fixed the flickering lines by only checking one relay per inactive vessel, and by setting BestVesselRelay per vessel in RelayDatabase.
Probably fixed the flickering lines by only checking one relay per inactive vessel, and by setting BestVesselRelay per vessel in RelayDatabase.

--- a/ARFlightController.cs
+++ b/ARFlightController.cs
@@ -241,6 +241,35 @@
 				FlightGlobals.ActiveVessel != null
 			)
 			{
+				Vessel vessel;
+				IAntennaRelay relay;
+				IList<IAntennaRelay> activeVesselRelays;
+
+				for (int vIdx = 0; vIdx < FlightGlobals.Vessels.Count; vIdx++)
+				{
+					vessel = FlightGlobals.Vessels[vIdx];
+
+					if (vessel == FlightGlobals.ActiveVessel)
+					{
+						continue;
+					}
+
+					relay = vessel.GetBestRelay();
+
+					if (relay != null)
+					{
+						relay.FindNearestRelay();
+					}
+				}
+
+				activeVesselRelays = RelayDatabase.Instance[FlightGlobals.ActiveVessel];
+				for (int rIdx = 0; rIdx < activeVesselRelays.Count; rIdx++)
+				{
+					relay = activeVesselRelays[rIdx];
+
+					relay.FindNearestRelay();
+				}
+
 				log.Append("Checking vessel relay status.\n");
 
 				this.currentConnectionStatus = FlightGlobals.ActiveVessel.GetConnectionStatus();

--- a/ARMapRenderer.cs
+++ b/ARMapRenderer.cs
@@ -26,8 +26,6 @@
 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-#define DEBUG
-
 #pragma warning disable 1591
 
 using KSP;
@@ -43,8 +41,15 @@
 		#region Fields
 		private Dictionary<Guid, LineRenderer> vesselLineRenderers;
 
+		// Debug Stuff
+		#pragma warning disable 649
+		private System.Diagnostics.Stopwatch timer;
+		private Tools.DebugLogger log;
+		private long relayStart;
+		private long start;
+		#pragma warning restore 649
+
 		#pragma warning disable 414
-		private bool dumpBool;
 		private Color thisColor;
 		#pragma warning restore 414
 		#endregion
@@ -91,12 +96,12 @@
 			{
 				this.vesselLineRenderers = new Dictionary<Guid, LineRenderer>();
 			}
-		}
-
-		#if DEBUG
-		private System.Diagnostics.Stopwatch timer = new System.Diagnostics.Stopwatch();
-		#endif
-		private Tools.DebugLogger log = Tools.DebugLogger.New(typeof(ARMapRenderer));
+
+			#if DEBUG
+			this.timer = new System.Diagnostics.Stopwatch();
+			this.log = Tools.DebugLogger.New(this);
+			#endif
+		}
 
 		private void OnPreCull()
 		{
@@ -109,7 +114,6 @@
 
 			#if DEBUG
 			timer.Restart();
-			long start;
 			#endif
 
 			try
@@ -134,9 +138,7 @@
 					{
 						Vessel vessel = FlightGlobals.Vessels[i];
 
-						#if DEBUG
 						log.AppendFormat("\nStarting check for vessel {0} at {1}ms", vessel, timer.ElapsedMilliseconds);
-						#endif
 
 						if (vessel == null)
 						{
@@ -157,29 +159,26 @@
 
 						log.AppendFormat("\n\tChecking vessel {0}.", vessel.vesselName);
 
-						#if DEBUG
 						start = timer.ElapsedMilliseconds;
-						#endif
 
 						IAntennaRelay vesselRelay = vessel.GetBestRelay();
 
-						#if DEBUG
-						log.AppendFormat("\n\tGot best relay {0} for vessel {1} in {2} ms",
-							vesselRelay, vessel, timer.ElapsedMilliseconds - start);
-						#endif
+						if (vesselRelay == null)
+						{
+							continue;
+						}
+
+						log.AppendFormat("\n\tGot best relay {0} ({3}) for vessel {1} in {2} ms",
+							vesselRelay, vessel, timer.ElapsedMilliseconds - start, vesselRelay.GetType().Name);
 
 						if (vesselRelay != null)
 						{
-							#if DEBUG
 							start = timer.ElapsedMilliseconds;
-							#endif
 
 							this.SetRelayVertices(vesselRelay);
 
-							#if DEBUG
 							log.AppendFormat("\n\tSet relay vertices for {0} in {1}ms",
 								vessel, timer.ElapsedMilliseconds - start);
-							#endif
 						}
 					}
 				}
@@ -208,12 +207,15 @@
 		#endregion
 
 		#region Utility
-		#if DEBUG
-		private long relayStart;
-		#endif
 		private void SetRelayVertices(IAntennaRelay relay)
 		{
 			log.AppendFormat("\n\t\tDrawing line for relay chain starting at {0}.", relay);
+
+			if (relay.vessel == null)
+			{
+				log.Append("\n\t\tvessel is null, bailing out");
+				return;
+			}
 
 			LineRenderer renderer = this[relay.vessel.id];
 			Vector3d start = ScaledSpace.LocalToScaledSpace(relay.vessel.GetWorldPos3D());

--- a/AntennaRelay.cs
+++ b/AntennaRelay.cs
@@ -111,8 +111,6 @@
 		{
 			get
 			{
-				//this.FindNearestRelay();
-
 				if (this.KerbinDirect || this.targetRelay == null)
 				{
 					return this.DistanceTo(Kerbin);
@@ -159,7 +157,6 @@
 		/// <returns><c>true</c> if this instance can transmit; otherwise, <c>false</c>.</returns>
 		public virtual bool CanTransmit()
 		{
-			//this.FindNearestRelay();
 			return this.canTransmit;
 		}
 
@@ -167,7 +164,7 @@
 		/// Finds the nearest relay.
 		/// </summary>
 		/// <returns>The nearest relay or null, if no relays in range.</returns>
-		private void FindNearestRelay()
+		public void FindNearestRelay()
 		{
 			if (!FlightGlobals.ready)
 			{
@@ -666,6 +663,8 @@
 		{
 			this.moduleRef = module;
 			this.isChecked = false;
+
+			Tools.PostLogMessage("{0}: constructed {1}", this.GetType().Name, this.ToString());
 		}
 	}
 }

--- a/IAntennaRelay.cs
+++ b/IAntennaRelay.cs
@@ -83,6 +83,8 @@
 		/// </summary>
 		bool CanTransmit();
 
+		void FindNearestRelay();
+
 		/// <summary>
 		/// Returns a <see cref="System.String"/> that represents the current <see cref="AntennaRange.IAntennaRelay"/>.
 		/// </summary>

--- a/ModuleLimitedDataTransmitter.cs
+++ b/ModuleLimitedDataTransmitter.cs
@@ -436,6 +436,14 @@
 			return this.relay.CanTransmit();
 		}
 
+		public void FindNearestRelay()
+		{
+			if (this.relay != null)
+			{
+				this.relay.FindNearestRelay();
+			}
+		}
+
 		/// <summary>
 		/// Override ModuleDataTransmitter.TransmitData to check against CanTransmit and fail out when CanTransmit
 		/// returns false.
@@ -444,6 +452,8 @@
 		/// <param name="callback">Callback function</param>
 		public new void TransmitData(List<ScienceData> dataQueue, Callback callback)
 		{
+			this.FindNearestRelay();
+
 			this.PreTransmit_SetPacketSize();
 			this.PreTransmit_SetPacketResourceCost();
 
@@ -558,6 +568,8 @@
 		/// </summary>
 		public new void StartTransmission()
 		{
+			this.FindNearestRelay();
+
 			PreTransmit_SetPacketSize ();
 			PreTransmit_SetPacketResourceCost ();
 

--- a/ProtoAntennaRelay.cs
+++ b/ProtoAntennaRelay.cs
@@ -54,6 +54,12 @@
 				}
 				else
 				{
+					Tools.PostLogMessage("{0}: Could not fetch vessel!  {1}{2}{3}",
+						this.ToString(),
+						this.protoPart == null ? "\n\tprotoPart=Null" : string.Empty,
+						this.protoPart != null && this.protoPart.pVesselRef == null ? "\n\tthis.protoPart.pVesselRef=Null" : string.Empty,
+						this.protoPart != null && this.protoPart.pVesselRef != null && this.protoPart.pVesselRef.vesselRef == null ? "\n\tthis.protoPart.pVesselRef.vesselRef=Null" : string.Empty
+					);
 					return null;
 				}
 			}
@@ -146,6 +152,8 @@
 		public ProtoAntennaRelay(IAntennaRelay prefabRelay, ProtoPartSnapshot pps) : base(prefabRelay)
 		{
 			this.protoPart = pps;
+
+			Tools.PostLogMessage("{0}: constructed {1}", this.GetType().Name, this.ToString());
 		}
 	}
 }

--- a/RelayDatabase.cs
+++ b/RelayDatabase.cs
@@ -143,6 +143,7 @@
 			}
 			else
 			{
+				var dump = this[vessel];
 				return null;
 			}
 		}
@@ -358,7 +359,7 @@
 								module
 							));
 
-							relay = (module as IAntennaRelay);
+							relay = new ProtoAntennaRelay(module as IAntennaRelay, pps);
 
 							if (relay.maxTransmitDistance > bestRelayRange)
 							{
@@ -367,7 +368,7 @@
 							}
 
 							// ...build a new ProtoAntennaRelay and add it to the table
-							relays.Add(new ProtoAntennaRelay(relay, pps));
+							relays.Add(relay);
 							// ...neglect relay objects after the first in each part.
 							break;
 						}

--- a/RelayExtensions.cs
+++ b/RelayExtensions.cs
@@ -166,45 +166,7 @@
 		/// <param name="vessel">This <see cref="Vessel"/></param>
 		public static IAntennaRelay GetBestRelay(this Vessel vessel)
 		{
-			BestVesselRelayCache relayCache;
-
-			if (RelayDatabase.Instance.TryGetBestVesselRelay(vessel, out relayCache))
-			{
-				if (
-					AntennaRelay.searchTimer.ElapsedMilliseconds - relayCache.timeStamp <
-					AntennaRelay.millisecondsBetweenSearches
-				)
-				{
-					return relayCache.relay;
-				}
-			}
-			else
-			{
-				relayCache = new BestVesselRelayCache();
-				relayCache.vessel = vessel;
-				RelayDatabase.Instance.SetBestVesselRelay(vessel, relayCache);
-			}
-
-			double bestScore = double.PositiveInfinity;
-			double relayScore = double.NaN;
-
-			IList<IAntennaRelay> vesselRelays = RelayDatabase.Instance[vessel];
-			IAntennaRelay relay;
-			for (int rIdx = 0; rIdx < vesselRelays.Count; rIdx++)
-			{
-				relay = vesselRelays[rIdx];
-				relayScore = relay.transmitDistance / relay.maxTransmitDistance;
-
-				if (relayScore < bestScore)
-				{
-					bestScore = relayScore;
-					relayCache.relay = relay;
-				}
-			}
-
-			relayCache.timeStamp = AntennaRelay.searchTimer.ElapsedMilliseconds;
-
-			return relayCache.relay;
+			return RelayDatabase.Instance.GetBestVesselRelay(vessel);
 		}
 	}