i had basically the exact same issue. 2 guns, etc. Here's what I did:
I got a new, different version firmware file from Andy (warne) that seemed to help some. Also, when I had a hard time getting a calibration, I completely darkened the room (unfortunately working in a room with windows I couldn't easily cover, so it was done at night. Took one shell off the gun and took off the front smoked lens. then, calibrated successfully and put the gun back together. All IR led signals tested fine throughout-not the problem. Never been calibrated since and no complaints from the user. More detail can be provided if needed. I don't have this rig here anymore to look at.