I don't know if anyone is monitoring this thread, but I hope so, because I would REALLY like the Supply Wagon to be fixed. In anycase, I hope this information may help.
I like having a castle that is out of the way and doesn't come under attack often, so I usually conquer a castle before Swearing my Oath to a king. I noticed my Supply Wagon stop functioning properly (with the Invalid Item error and disappearing from the game) after I swore vassalage. Fortunately, I save a lot, and was able to go back to several different stages. What I found was this: If I destroyed the Supply Wagon... Became King... Swore Vassalage... and then re-built my Supply Wagon, it seemed to work okay; other than the Color remaining as Rebel Red.
The other thing I noticed with the Supply Wagon, before it would get the "Invalid Item Error" is that it would be labelled as the Name of My Kingdom, which no longer existed.
I believe what is happening is: When the Supply Wagon is first created it is a Caravan Under the Player; when you become King (or swear vassalage), it becomes a Caravan Under Your Kingdom... but once you are no longer a king, and your Kingdom no longer exist, Your Supply Wagon, Still being listed as a Caravan under your kingdom, because the Invalid Item. I also tried Destroying and re-building the caravan after swearing vassalage, but got the same error. The only time it worked "Close to Correctly" was by getting rid of it, before I became King, and re-building it after my Kingdom was gone. NOTE: I didn't do a lot of testing here; I Destroyed the Cart, Conquered a castle, Swore Vassalage, Sent the Wagon on a Run, It returned and I was done; happy with the fact that I may have found a 'Quick Fix', and would only have to throw away about 2 Game Weeks of work, since I had spent that time just finding troops for the castle before even realizing there was a problem.
Also, someone stated that Sending a Gift May have been a part of the problem; I haven't sent any gifts to anyone throughout this game.
On a slightly different note; thus far I have not had the issue where the Supply Wagon was stalking; however, there was a case in which the Supply Wagon wouldn't re-join (I kept telling it I didn't have room). I believe this occurred because at the time I had more prisoners than I was allowed to hold; which was (I think) due to hurt soldiers and the loss of men after a fight; but once we rested the number went back up, and the supply wagon joined. Had a similar issue happen once with Spies after a Skirmish where they had captured Prisoners and I had not attached my prisoners to the Supply Wagon yet.
I hope any of this or all of this may help. We mustn't lose the Supply Wagon: of all the great features in this Mod... this is in the Top 5!!!!