How old is the PEQ's pack 4.0? If it's as old as I think it is, you might want to try a newer revision. (The bot's do "disappear" when you group another player on the current revision too, but there have been quite a few revisions to the code that make it worth-while to upgrade.)
The newest pre-compiled servers can always be found here:
http://code.google.com/p/projecteqemu/downloads/list