I have been having problems once in awhile with stubborn u-joints. I will get it all set up in the press, and have a lot of trouble with some of them, and after a lot of pressure they finally bust loose. Everything after that goes well, except sometimes I have trouble getting the retainer clips back in. Usually I force them in, sometimes they are so tight they will not sit flat against the end of the u-joint cup.
After having this problem off and on several times over the years, I think I have discovered what is causing it; When I have a stubborn rusted u-joint, and I put a lot of pressure on it in the press, if it happens to be the top side cup that is stuck, the press is actually bending the yoke arms together a little bit as I am cranking down on them in the press. The bottom cup moves, the top one doesn't, so it's bending them together slightly. This is what is making my clips difficult to get back in place.
It's almost like you need a small u-shaped support to slide inbetween the yoke arms to support them while you put pressure on it, much like the support jig they make for a-arms when you are pressing a-arm bushings in place. Have you guys ever experienced this problem?