Are there any compiler arguments that will make the resulting .swf file come out identically each time? For example if I compile a C program and then five minutes late compile that same C program comparing the resulting binary with md5 it is identical. Conversely if I compile an mxml file to a swf and 5 minutes later compile that same swf it isn't identical.
Have you tried restarting FCSH, or, better yet compiling from command line bypassing the shell? Are you compiling framework files (doesn't matter if they are only AS3 or both MXML and AS3), if so had you tried to find any differences in the generated code? I'm asking this because, generally, this shouldn't happen... unless... I don't know, maybe compiler puts some metadata, like compile time, but that would be just strange...