You may be on to something.
If that was the last step that affected the problem...
The ears in the slip yoke and/or pinion flange can go out of round when a ujoint wears out or gets overdriven on installation. Or one or more of the machined stops for the caps, which are barely there to begin with, get mauled. Or those ears get tweaked. The latter two are especially easy to do (the flange is more likely to bend than the yoke, though) if you press the joint out rather than using the bfh technique and back the cap out. You basically end up with a round peg in an oval hole. It's not much, might not even be enough to see, but it won't drive altogether right. Been there, done that, got the tshirt.