Hey Pixel,
I have worked on a lot of large projects and haven't run into this before. I am inclined to think that it is a problem with your code but you might be right. If you are sure you should definitely lodge a bug report.
What I normally do when I run into something that 'should' be working but isn't is to place stops in your connecting events so you can inspect what all the variables are at each point. So if you have an event that handles saving or loading, disable your function call or whatever style you use to link events and see if it is consistent.
Thanks GG it was a wierd bug and I never seen it before. But it happened right in front of me so thats how I knew it wasn't me. I just posted this just in case someone else encounters their save variable changing when they save, so they don't go nuts. I know when I was a beginner I would go crazy just to find out it was something simple. Now that Iam experience I don't go crazy , I slow down so that I can double check everything.