If you are building a server using the latest PEQ database, you need to be sure to use a matching version of the emulator code. The ones in the download section of this site are way outdated and probably won't be updated any time soon. We have a new site here for downloads:
http://code.google.com/p/projecteqemu/
Updates are very frequent there, which is why we haven't had the download section of this site updated in a while. Even if it was updated, it would be outdated quickly at the rate changes have been coming in. In the couple months since the new SVN was added, we already have over 200 change updates including hundreds of changes.
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