Sounds like it's one of a few items, but first question is are you using a stock fuel pump in tank or are you running any aftermarket fuel upgrades (pump wise)?
- It could be the pin out is different on the actual ECU vs the EMS. I'd check the wiring and the AEM wiring diagram/pinout locations and verify this is correct
- It could be a setting on the AEM, have you gone through and set up what pump your using and where it is wiring wise to which pin-out? Such as priming/and running options?
I would start there because it has to be either a wiring issue or AEM programming/setup issue.
Don't recall if there is any difference in wiring in the Auto/manual (I would imagine not) and if there isn't its a wiring into the EMS/setup problem.