However, I found it still occurs even without that. The XP bar will be visible while getting on the plane and during the cutscene before the in-game conversation menu with delara. At first I thought it happened if you still had the XP bar visible in the cutscene - you can force this by using the Typhoon on the two turrets and killing guererro, then quickly getting on the plane. This is why I had to test it so much, because no matter what I did in game it happened seemingly at random. If you got on the plane too soon after the choke effect has last happened, it will not happen during the cutscene.
The timer does not tick down while in a menu, nor when in third person view during a conversation, because time is frozen. After around 15 seconds of standing around the choke effect plays, then around 20 seconds after that the choke happens again, then again a couple seconds after, then the loop repeats. The trick is that the screen glitching from the choke does not happen randomly, it's on a looped timer. The screen glitching graphic played in the short cutscene of delara asking jensen what happened, the one that plays right after the one of you getting on the plane and before you enter the in-game graphics conversation with delara. I tested with every possible combination of endings I could think of: Save fixer, save meijia, save both, or kill them both, all 4 with altered biocell or no biocell. I suffered a lot of loading screens to be able to tell you this, and I'm just as disappointed as you will be: It's a UI glitch. I assume you mean when the screen shakes and glitches out, like when you try to use an aug with the TYM chip in and experience "the choke"?