I'll definitely defer to your wisdom regarding my theory. I'm nowhere near as experienced with all of this as you are - I'm just a bit of a math nut who can find patterns (sometimes where there isn't even meant to be one to find).
The 3 frame shift does actually make sense of what I've been seeing in TMT, however. A lot of times the subtitle will suddenly adjust depth just before it stops being displayed (another thing which makes it less-than-desirable for 3D playback) - and that jump corresponds to the depth of the following subtitle. Presumably that also corresponds with a scene cut but I can't actually say I've paid that much attention to it. Because they don't seem to like frame-by-frame viewing I've never been able to get an accurate count of exactly how long that shift lasts but 3 frames isn't outside the realm of possibility. Sadly, I've no way to determine whether any have ever been over 5 because it really is just a fraction of a second, plus it is a little jarring to watch.
I look forward to testing the results of your new methods. A couple of titles have given me slightly off results so far, soI've got a baseline to test against.
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