Well I figured out a work-around isn’t necessarily optimal but does gets the job done (I’m on Mac OS X Snow Leopard).
1. Quit AE if it is open.
2. Change system language to Japanese by going to System Preferences… -> Language & Text -> drag Japanese (this one: 日本語) to the top of the list.
3. Don’t log out or anything, next just launch AE.
4. Open the project with Japanese characters in AE and you will see that it should all work now.
5. If you were to log out and then back in, your whole system will be in Japanese and you may find yourself lost. The good part is you can go back to System Preferences now and change it back so that English is back at the top of the list. Now as long as AE is open those Japanese files will still work.
The only drawback is that AE sort of half thinks your system language is in Japanese. All the AE menus are in English, but system dialogue boxes like Save As… or Import… come up in partial Japanese. This is definitely not optimal but it does work so I hope this helps anyone who comes across this issue. If anyone out there has an actual solution I’d love to hear it!
Thanks!
~Matt