The bug (yes, I think of it as a bug) that Jim refers to is because After Effects increments numbers at the ends of file names when it saves a copy. But the dynamic link doesn't catch that and then refers to the wrong version.
We added a preference in CS6 to get around this problem. It's a preference because we didn't want to break people's exisiting workflows.
There will be more information about this forthcoming as we put out the details of the CS6 software over the next few weeks.
Ok, so removing all numbers from my AE projects seems to have worked. I didn't have incremental numbering at the end of my files, but I had numbers at the beginning to order them for myself, followed by a bit of the script text (1- In the busieness world, 2- a lot of professionals, etc.).
I haven't tried this on the other project that was having the most of the issues, but this did solve the problem on my second project, so I imagine it would fix the other as well.
Thanks a lot everyone!