I would say the problem lies in the joint itself. Either the Pin is installed off center, the tapping of the shaft is off center, or the pilot itself is off center and pushing off to one side or the other.
Many times, cue makers will do the pin install, then tap the shaft , then cut the pilot many days apart. When doing this, if the head stock has any play or anything was on the head stock allowing the shaft to not be in the same position as the original tapping, the pilot will end up off center.
To check, turn the shaft in the head stock and dial indicate the pilot to start with. I would guess this is your problem. If it is, using a true drive pin to center the shaft accurately , you can shave the pilot as needed until the pilot is clear of hitting any sides while screwing the cue together.
If the pilot is not the problem, I would soon guess indicating the pin itself with the same technic. If the pin is off, a new pin will need to be installed.
And in some cases, look for clear coat that has not been removed on the facing itself.