Hey,
I was having a similar problem with AE CS4 in regards to auto-saving… It seemed that the problem was that when I was clicking Ctrl+S it was saving into the last Auto-Save file as opposed to the original AEP. When I opened up my original project the next day (which I thought I had saved), I was missing work because it wasn’t the most recent project file. Can’t remember CS3 ever having this problem… unless it’s a problem with my auto-save prefs. Any ideas?