I just did the BB3 upgrade by replacing the NXT2 box on my BB2E with the NXT3.2 CPU and used the upgrade power cable for the power input to the NXT3.2 box which the NXT2 doesn't have.
No video issues at all. The only thing I had to do was replace the VGA>VGA cable that went to the top monitor with a DVI>DVI cable to connect DVI instead of VGA to the top monitor, which is specified in the upgrade guide. Can't use the VGA port on the NXT3.2 CPU. DVI port in the back is secondary (top monitor), DVI port in front of it is the primary display.
Everything came up ok, I've had no video issues whatsoever and didn't even need to change any jumpers.