See if you notice that it happens only after the first map changes to a new map. If that is exactly when it happens there is a setting in your UT2004.ini that might need to be changed:
bRestartServerOnPortSwap=True <---------------- Set this to False.
I'm no master of running a server but I run a few and this is what I think your issue may be. I certainly invite others to jump in with helpful suggestions too.
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~Peace~
Hermskii
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