The "vaunted" STL was first to open and transform my Voyager prime and he wasn't aware of the gimmick and just folded down the legs thinking it was ratchetingThe figure never recovered. It also had the same very loose chest/shoulder pins. I exchanged it for another.
Anyway, I spent a good bit of time trying to learn and understand how to transform the waist perfectly back in to alt mode, and for me, it works pefectly now. If you are facing prime, keep his chest facing you and turn his legs 90 degrees so that you are looking at the right side of his right leg. This is the point that you flick the waist back and start the rotation. As Kurdt says, at about the last 180 degrees, you have to hold the latch button in so it doesn't obstruct the remaining rotation. It works perfectly (no clicking) for me now AND I am lucky enough to have non-loose shoulders, so my opinion of this figure has grown.