I don't know what you have in terms of installation software, but try to run the installation program for AE. You will hopefully be asked if you want to uninstall or repair the program, in which case you choose the latter. If AE was installed as part of the Creative Suite (rather than a stand-alone program) go back to the first CS disk, pop that in and you should be prompted for an uninstall/repair action from there.
In my own experience, when an Adobe program gets that unhappy with itself, a repair via disc is one of the only things which works (short of a complete uninstall and re-install). There is a chance you will have to uninstall either AE itself or the entire Suite to resolve the issue, but that's a worst-case scenario.
Based on your most recent report about weird Photoshop errors and suchlike, however, it does kind of sound like maybe settings on something other than the software got a little tweaked out (which is now causing the software to tweak out). If you check your Preferences in Photoshop (you have CS4?), you should find something about disabling/enabling GPU enhancements. Maybe try playing around with those? I don't have CS4 in front of me at the moment, so I'm sorry I can't be more specific.