Hey JM,
I am also interested in your question since I got the same problem.
When changing the focus screen of my K10D to an microprism screen and then back to the original screen, the red focusing rectangle was shited a bit to the right.
I was searching the forum and all I found out is that sending the camera in for service is the only option which might fix this.
It seems as the LED which reflects the light on the focus screen might be slightly misaligned, I guess as result of my amateur-like focus screen exchange.
The LED rectangle is separate from the actual focusing area. So you still have to focus at the center of the focus screen instead of the shifted red LED area, as I understand it. There is no problem in using the camera as usual, the focus is not affected by this afaik, its just damn annoying xD.
Hope this helps a bit, if you find a solution please let me know
.
Best regards