I am having a very similar problem. But sometimes when I do finally save it, omedit will somehow corrupt my model so if it loads it does not function the way it did right before I exited.

I have a large modelica package that I am trying to edit in openModelica. I have version 1.8.1 and am running on windows 7. I can open the package just fine and can edit the package just fine. After I edit I even check the model for the part that I edited and everything checks out ok. I then save the whole package, and despite taking excessivly long to save a two megabyte file it eventually does save it. However if I then try to reopen the package it will complain that there is an unexpected semicolon. Looking at the file in a text editor it is apparent that every where there is an unexpected semicolon is a line that looks like:
annotation;
I can remove these lines and the package will load. But when I simulate a model using components from this package it will generate very wrong results. Even if I only use components which I did not edit. In fact my model breaks in this way even if the only edits I make to the package are moving items around but not changing connections. Does anyone have any idea why this might happen?