Ya know I had this same problem and the Stuffit pref change didn't work. I even went as far as trashing the prefs then trashing the App and all related files and doing a reinstall. Still nothing worked. Then I found UT Converter 2.0 and no matter how Stuffit garbles my files, I just drop them on the converter and they are good to go.
I strongly recomend it to all Mac UT players. Too bad I don't remember where I downloaded it. Anyone have a link?