Update:
"...and that the best solution would be to wipe the disk, reinstall the OS, and do fresh installs on all apps. I may do that if I run into any more problems."
*May* do that...? Ummm... <ahem> I firmly believe that you *must* do that to avoid all sorts of maddening Mac nonsense, as a matter of Standard Operating Procedure. Especially on any sort of a production machine, in any creative environment. You've already wasted more time on this *one* problem than it would take to do it right. Don't wait for the next "gotcha" to jump out and bite you! Or your Client.
I do a Clean Install, once a year (or so), whether I need it or not. Keeps the gremlins at bay. And that forces me to do a Full Backup in the process.
Cheers,
--Charles