I'm having the exact same problem on my dedicated server.
I'm experiencing lag a few minutes after the mission has started. It's starts at 1 ms, and after a while (1-2 minutes) it can increase  up to 2000+ ms.
While playing I ran ping in a cmdprompt.This is what I got:
(hope u'll understand my graph )
time/ms-------------------------------->
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V
From 1 ms to 2000+ ms and back to 1 ms again, and this patern repeats itself over and over.
CPU/RAM load stays the same, about 30%/330MB with the mission I was testing.
And also my network isn't getting higher then 50KB/s.
So whats the problem here? Plenty of CPU, RAM and bandwith available...
Server specs:
Celeron 2.7 Ghz
1GB Ram
100 Mbit connection
Desktop specs:
AMD 4200 X2
7800 GTX
1GB Ram
1000 Mbit connection
