>I use Eudora all the time and it doesn't keep messages as separate files in the folders - but cant get Thunderbird to work -I cant open the folders

I just remember some eversion of Eudora did so, 20 years ago (and that was the main reason I uninstalled it the same day).

As for Thunderbird... try to set your folders to reside in a non-default location. Windows may interfere if it's there, and you shouldn't hold your emails on c: drive anyway, never was healthy.