GK Encoding time

When I first built this PC I could encode with Gordian Knot 0.35 at 99 fps (with Trend antivirus working), now the best I get is 67 fps. The 99fps was reading and writing to a Vantec Removable SATA HDD, that deteriorated over time to 67 fps average. Now I read and write to my primary HDD (also SATA) and the result is no better. I have defragmented and crap cleaned etc, cleared cache etc. I was thinking the only solution would be to reinstall XP operating system to get back to the faster encoding times? I have a Core 2 6600 with 2 gig RAM, Asus MB. I tried AutoGK and no improvement. I tried increasing the page file size from 2000 MB to 4096 MB and no improvement. I tried encoding with Xvid and no improvement. Please help.