I am having the exact same problem on a PC. It seems that copying/pasting all frames into a new FLA fixes the issue. It's as if the FLA becomes corrupted after awhile, but only in this respect. WE NEED A FIX!!!
I have found a solution to my problem. I don't know why it works but I found online that if you export your swc's and swf' into a different directory from your fla files, publish will work. So if you have your fla files in a directory called 'work' go to your publish settings and make sure the swf export directory is something like 'work/lib' or 'work/swf' and it will publish it to that folder. I think you have to create that folder manually before exporting it as well. hope this helps