I'm having the same issue. I think it's related to the AE vs TPS table, which by default, kills all AE above something like 3000 rpm. I have just flattened that table, no lower than 100%, and will try that.
I am New to Holley Fuel Injection and am having a problem with the motor accelerating after coming off the two step. I am running a LS1 in a super stocker and when i release the trans brake teh car just doesn't leave for a couple of tens and the runs well the rest of the run. I assume I am lean coming off the two step and then the correction catches up and runs ok from there on. any Ideas where to look.