I've seen that problem at some point too. It's most likely caused by rail-layer driving over diagonal track (the version you're using has some serious flaws in that area, there's an updated version here: https://forums.factorio.com/forum/vie ... =80#p48654 ) No idea if it's fixable without any low level hacking though, I just went back to an earlier save and made sure to avoid diagonal track with that version of rail-layer.
I don't have OCD, I have CDO. It's the same, but with the letters in the correct order.
The problem were some "double rails". Some of the rails created by mod were created on the exactly same place (with same direction) as existing rails, this is something the engine isn't prepare for so these are the steps that I made.
1) When loading older save, the double rails are removed.
2) Segments are rebuild for older saves as well, so the save is loadable again.
3) Script can no longer create double rails.
So your game is now working without problems in 0.11.0,