My response is that I assumed you don't have the MBC. If you're saying you got the readings from your boost gauge and the AP, would that be a faulty boost sensor? If you use "read live boost" function on AP, it basically reads whatever boost signal received by the ECU at the boost sensor.
BTW, what version is your map? Also, when you upload your map from your PC to AP by the Cobb Map Management software, does the selection under "ECU Identifier" matches to your actual ECU Identifier? I got my AP off eBay, and the previous user was 2004 MT, so I need to change it to 2004 AT (AH802) before initialization. (I didn't know they have 2 identifiers, AH801 and AH802 for 2004 4eat WRX, so I searched mine from the ECU case.)