Facing or bent pin as mentioned would be my guess as well. Another thing that can happen with a bent pin is It can knock the centering off, and the matching of the shaft to the handle off to one side. This can also happen when a pin is not installed straight, and You go to add a aftermarket shaft, that hasn't just been sanded or had the finish built up to match.
I recently had one to match a used shaft from the same maker of the handle, the Shaft I needed to match was the correct thread count, but needed opened up with a tap to fit the threads, as the fit was too snug when screwing the shaft on. The guy ( a good friend of mine) had a aftermarket low deflection shaft he got when he bought the handle,but I only had the handle in my possession at the time I was doing the work. It rolled nicely on a table, but the collars were not lining up perfectly. I stuck the handle in the lathe indicated the OD of the collar and zeroed It in, and sure enough the pin was bouncing all over the place after wards. I called the guy told Him of the problem, I told Him that the match was not that bad off, In fact so minor that he may not even had noticed, but that i just notice things like that, and asked him if the aftermarket shaft had that same problem, because from what I was seeing It should. He proceeded to tell me that It did not, and he would notice that as He checks for those things, knowing Him and having watched him check for that on other cues before, had me thinking well maybe for what ever reason the other shaft wasn't off as bad, so My response was, well I'll have to show You because some people may not detect this. I met up with Him, showed him what I was talking about, he rolled the cue out and said he wasn't even worried about fixing it because the centering wasn't enough to concern Him, and it did roll really straight together for the most part, although he did see what I was talking about. We had a few beers that afternoon, and played a few racks on his table at home, so while I was there I asked to see the aftermarket shaft for my own piece of mind, and sure enough It was off the exact same amount on the same side.
Anyway My point is if you suspect a bent been check to see how well the collars match up, as that can be another indicator.
