My PC has no issues with any other MMOs and I played STO from beta back in the day on the same rig no issues at all.
From memory it is:
AMD 2.6 Dual core
Nvidea 8600 GT 256mb
Windows XP Pro
Using windows own firewall and STO on exceptions positive list.
Anti-virus is Avast.
I will try disabling the on demand downloading too.
FWIW, your system may just be overtaxed. Sometimes this type of issue can be fixed by reinstalling the game. But even at STO's modest requirements, you may be doing too much for the computer to handle.