First, it sounds like you are just not holding the flute properly. Far too often, I see players using saddles because they simply were never taught the proper way to hold a flute. I'd suggest taking a few lessons from a flute teacher who can help you adjust your hand position. That may also help with your tendonitis and carpal tunnel issues.
Second, take the flute to a repair shop. It sounds like a screw may have been a bit loose or perhaps a post is slightly bent out of alignment. In normal use, the mechanism sound not pop out of place unless you have a grip like Iron Man.