In your injector phasing setup, make sure you are going down in your progression through your firing order. For example...
Firing order 1-2-3-4-5-6
360 240 120 0 600 480 .......NOT 360 480 600 0 120 240
The next cylinder to fire is based on TDC#1 and it fires later, so LESS degrees before TDC.
Some of the base maps were set up incorrectly, so check this in your calibrations.