Managed to fix it. I went through the AVIsynth plug-ins folder, and deleted any duplicates there which might exist for other CPUs.
I also downloaded a different mt_masktools.dll (dated 27th Jan '06) from http://manao4.free.fr/
Lastly I ran my test clip through DGIndex again and created a fresh D2V file.
One or all of these seemed to do the trick!
Fingers crossed it will work for you as well :)