Seems that there was something different wrong.
Because of the fact that auto-discovery of MySQL-Tables on about 5 servers with about 200 Databases each made HQ doing very strange things and also made the server where HQ-server ran, nearly unusable.
IMHO there seems to be too complex checking of each DB/table which brings the server (P4 1,6 GHz, 1GB RAM) nearly down.
After doing a complete re-install of the server and all clients, the problem with FTP connects went away.
Another thing is saw, was that HQ seems to open many connections to the database-server when monitoring databases and tables. Running the whole thing produced an error of MySQL which stated that there were too many connections.
Maybe this is another thing which happens when the server gets overloaded OR it is a misfunction of HQ. I don't know, but it might be an issue the HQ-developers can have a look to.
Cheers
Tobias