I had the same problem on a commericial repeater which was a GE Exec II. The user radios were all Motorola M120. The modulation parameters were normal, although I don't remember just what they were at the time. Since the radios did not have mic gain controls (maybe there was an adjustment in software, I don't know), I modified each radio so as to reduce the amount of mic audio getting to the transmitter audio circuit. I had no problems after that.
Laryn K8TVZ