iGyro and subtrim function

• I had used sub trim to adjust the neutral position of one of my elevator servos. I installed the iGyro and had several flights with it without incident. I decide to remove the subtrim and adjust the one elevator manually which I did. However, when I tested the system, that elevator has reversed direction. Upon reentering the same amount of subtrim, the one elevator went back to working in the correct direction. This is scary. What the problem that I should never use subtrim with the iGyro or what?