I would suggest putting the agent in a another db and have it reach out to all the mail*.box on the server.  My guess is compact of the mail.box(s) screws up the scheduled agent.

I will give it a try and post tomorrow if it was successfull.

At 1 am it does a re cache of scheduled agents against all .nsf   Since you put the agent in .box it does not see it.   My suggestion of moving it to a .nsf will work 

this happened to me before, archiving agents stopped working after midnight and i found out it was some agent refresh cache of some sort that domino runs at around midnight and because of other problems we were having with the server at that time (db problems caused by backup), i just configured an event handler to restart amgr when it sees the error (comes up right after midnight, which was an indication for us that the agents will stop running). so essentially, i was auto restarting amgr after midnight until our domino problem was fixed. 

I placed the Agent in a .nsf as suggested and problems were gone.

Also good was the question for the server record. In the "Server Tasks/Agent Manager"-Tab we have an entry "Refresh agent cache" with a Value of "00:00". It seems to me that it refreshes all scheduling and doesn't look at the .box Files.

Thank you all for your replies and suggestions.