QUOTE
Eudora has a primitive SPAM filter and in addition, I use SpamSieve as my primary filter.
If I'm not mistaken, SpamSieve replaces Eudora SPAM filters. SS sees the messages before Eudora does so your Eudora SPAM filters are never needed. They will be used, of course, to sort messages to the particular mailbox you want.
But it sounds like the filters are not really the problem, anyway. It might be possible to send all your known good addresses to SS so it can build a DB of stuff you want admitted. But you also have that capability when you find a 'false negative.' If there are so few of those that might be the easiest method, then follow Mayo's suggestion and don't bother checking the Junk box. It might also help to have those messages deleted in a shorter period of time than whatever you may be using...something like one day?