I'm using AE CS5 and am downloading the new patch as I type this but my internet connection is pretty slow, so I thought I should check on this problem in case it's not patch related and I'm doing something wrong.
I was working on some simple animated tables, each the same size. I created the first one and worked with it until happy and saved the project as table1. I then saved it as table2 and made changes to the text, effects, timing, etc. and did the same for a total of four tables.
Earlier I tried to open table2, it flashed up the correct table for a second and then displayed table1 and then AE crashed without any error. I get the same with table4, which flashed then displayed table3 and crashed AE. When I open table2 now the content is identical to table1. When I open table4, the content is table3. Somehow, using "save as" seems to have left some sort of link to the original file.
I had imported all four comps into PPro before this strange behaviour started but I doubt this is the cause. The "broken" project comps displayed as "media offline" in PPro.
You probably caused a loopy Dynamic Link connection that did not create separate files, i.e. invoked DL by adding one comp in Premiere, and then kept working on the original project in AE. Naturally, Premiere would then not have any idea about your intention to use other files/ comps....