It may have not been the MB it may have been chipset driver. Was it the exact same MB? I can also be the position of the RAM, it is possible that a slower piece of RAM was in the first slot and it was causing a issue. Even the exact same RAM can have a minor difference.
Since 8.1 is a little different the OS could be faster causing an issue that was always there but not showing up. There could have been a little extra heat the was effecting the CPU to.
Were these CPUs over locked?
I have seen this issue caused by OC, virus software, display drivers, PSUs and hard drive failures. If you used the same drive and did a format when the MB was changed bad sectors could have been marked or repaired that didn't get picked up before.
I have also seen the NICs cause this. The only solution in one case was to disable the onboard LAN in the BIOS