This might help you. My friend had a similar problem with Eudora5 after upgrading to OS9.1. Strange thing, my prefs on the same machine worked fine for the same popserver. We removed his preferences file, and he set his prefs a new, after that it worked. We kept his mailboxes and everything except the Eudora Prefs.
We also compared his old prefs with the new ones, but couldn't find much differences, except the box Overlap commands was now unchecked, so you may try this first, but i'm not sure if that helps. Overlap commands is in the checking mail chapter of the settings.