The MAP sensors are often not matched exactly. You can read the voltages when the engine is stopped and then try to balance and adjust for this difference.
I've found using the MAP sensors to balance is very frustrating. TuneECU only updates the display every 1/2 second or so. Also, the values jump all over the place. I can balance with an electronic gage in 2 minutes and know it is right on. I've spent a half hour with the MAP sensors and couldn't tell if it was balanced or not.
"Dad, can I get a motorcycle when I grow up?"
"Son, you can't do both"