Hey, just wanted to note a little update on that issue.

It seems, that the dedicated server does not like one part of our mod, the "blood patch" that inserts bloodeffects on playerhits. Without the Bloody_server.zip/_client.zip files it works perfectly, but we can't figure out, why the server hates us when we include the blood-files.
The server works now when the blood-files are included in the common/effects files. (original patch was taken from bf2)

Anyways, thank you for your help and this nice server-tool.