When an application is exited, it saves a preference file that records user preferences and such things as recently opened files, window layout when app was closed, etc. Sometimes this file can get corrupted which results in strange and unpredictable behavior.
Where it resides depends on the AE version and operating system you are using. It’s different for OSX and Windows and for 6.5 and 7.
You can do a search for a file that includes PREFS as part of its name.
Jim Kanter,
Digital Film Institute
http://www.dfilminst.com