Noise in the pulse counter wiring would be my first guess? Please describe the wiring to the actuator, what type of actuator, wire gauges, shielding, grounding etc... I'm sure there are smarter ones than me here that can also help get to the bottom of this situation. Electrical noise would make some counts get lost on the way back to the position you are going for, then the dish would be in wrong spot. Motor and sensor wires in the same bundle is the cause I have seen here mostly.
I'm using the standard "ribbon" cable. By that, I mean there's 2 coax runs, and motor wire bundle and a polarator bundle. The actuator pulse counter is in the same bundle as the motor power wiring. The polarator wiring isn't used because I'm using LNBF's. As for grounding, all my outside stuff is single point grounded to the power company ground rod. I've tried attaching the motor wire bundle shield to a ground terminal at both ends, then just one end, and then no connection at either end - doesn't fix my problem. A different make/model actuator has been tried also. I've even tried using decoupling capacitors. I had this same problem on both my old Paraclipse 12 footer and my newer KTI 12 footer also. One would think that the count wouldn't be so far off that the signal would be lost. The count is off by 2-5 counts (9% to 22.5%). The pulse count averages to 22.17 counts per degree for the KTI using a Gbox. One thing I haven't tried is using the polarator wiring for the actuator pulse count. But, being the pessimist that I am, I don't expect that to fix my problem either.