I have this problem as well and it is very frustrating. I am working with complex equations in model building and it take quite a while to get them correct. To have changes not save costs me a great deal of time. Something that should take 1 min takes an hour sometimes depending on what was changed. Why has ESRI not chimed in on this thread? Is there something we can do to get their attention? I do not make changes in ArcCatalog or have it open so I don't think that is causing the problem. It seems like "maybe" a certain state is remembered and changes are not saved beyond that step. In some cases it is just a couple differences. In other cases it goes back to a version from a year ago. I will try to cut and past the existing model into at new window and save it as a new tool and see if that fixes the problem. This does not seem to be widespread since it was hard to find the problem in other forums. I wonder what it is.
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