Problem solved In case of anyone stumbling upon this thread with a similar issue, this is where I found the fix http://sto-forum.perfectworld.com/showthread.php?p=5279681#post5279681
I posted another thread before I saw this, but seems this is pretty much the exact problem I am having aswell, with a similar setup (i7 3770, 16GB RAM, GTX560Ti, SSD). I've raised a ticket but no solution as yet. Gonna try the NIC driver fix as suggested when I get home, fingers crossed!
Thanks for the suggestion, though I fear thats not it. Playing other online games, streaming from Netflix and such are all working at full speed, it's only on STO that I have the issue.