There’s a point, as a non-Quicktime person, where I have nothing to add.
I do, though, make loops in h.264 with AME, working from Premiere, and they do run glitch-free. A client’s recent trade show demo was just one example, using a combination of 4K and 1080P footage and some fairly heavy (at least render-wise) graphics.
One thing I tend to do when I’m making a loop is to make the first and last frames by cutting a graphic and putting the tail end of it at the head end of the sequence, so there’s a still frame used in the transition. I’ve done it that way for a while now with no issues, and maybe that’s part of a good approach. Do you do your loops in that way?