You might look at CPU utilization, some other task may be hogging your machines resources (SMS in a corporate environment along with antivirus are good candidates).
I don't think the 52.16 drivers are setup for IV. I would go with 44.72, keep in mind 45.28 had some regressions so those could still be in the 52.16. You also need to make sure you have the September hardware lib installed.
Finally, corrupt acis bodies OR lots of arrayed features could cause some serious performance issues.
Probably unrelated but make sure you have all the latest chipset (including USB, AGP, IDE etc) , network, and audio drivers for your new motherboard installed. Something as stupid as an audio driver can be buggy and hog CPU cycles.