If you were commanding 12.7 via PE before and seeing a commanded of 11.7 in the scanner, then there was something else adding to your EQ ratio. Check your cat over temp protection, as it is one of the usual suspects in that arena.

 

If you still have cats and are trying to get your A/F dialed in then disable COT protection as that will throw it off.After you get the VE and MAF tables dialed in then enable your COT if you want.I know you already know this but if you are still running your MAF then your MAF table needs to be dialed in order for the PE table to be correct on what you are commanding.
Good luck buddy