You don't give any useful information for anyone to help, i.e. what revision of the server you are running and what revision of the database, what errors you are seeing in the files in the logs/ directory, but I'll take a guess at what your problem is.
If, for example, you download Revision x of the server source or executables, and have installed version y of the PEQ database, look here:
http://code.google.com/p/projecteqem.../utils/sql/svn
And source in each .sql file that has a prefix > x and <= y.
E.g. if you are running rev1264 of the server and you installed rev1052 of the PEQ database, source any sql files with a prefix between 1053 and 1264.
In particular, you most likely need this one for your NPCs to load:
http://code.google.com/p/projecteqem...kill_types.sql