I process my NEFs in ACR but when I go into Ultimate they look really bad with very muddy colours and blown highlight areas. I feel they are being processed again with Qimage's RAW processor as my jpgs are fine.
Paddy,
The issue seems to be normal.
When you process first in ACR, the adjustments you made are recognized by ACR only.
So what you see in Qimage when looking at the NEFs, is the un-altered raw files.
The same would happen in reverse.
If you process the images in Qimage Ultimate, REFINE, and sent that into CS5 or Lightroom, they wouldn't see the adjustments that Qimage Ultimate made.
If you find that you want to continue to use that routine, you need to convert your NEF + xmp file to a Tif.
Fred