There are two mods: the
Walkthrough Mod by JokerLeader and the
Walkthrough+ Mod by Emelex. Both of them modify some variables in the game in order to fix some old bugs and clean up some mess in the code of the original game. The original game does not know about these modified variables and may be confused by them. The second mod (WT+) modifies much more and gives you access to some old scenes or unused renders that have been deleted from the game. Saving your game during any of these scenes is guaranteed to confuse the original game.
If you have used a mod once, then in most cases your saved games will be permanently unusable with the original game. If you want to play your saved games, then you should only load them with the same mod, not with the original game nor with the other mod.
If you want to play the original game without a mod, then you should delete all saved games (at least all those that were saved with a mod) and start again from the beginning.