Wow, you caught it on video, and it matches very much the original description in reply #4. Nice! Still, I see a theory without bug for this video:
When you made the savestate, was the jumper already in the replay? The game prints the R in the corner throughout all of the early part of the video. When you savestate with an undone jumper in the replay, this jumper assignment will be preserved. When you stateload, such an assignment will be written back into the replay.
Speculation from reply #4: Bug might hit more often on huge maps. On larger maps, the game will run out of VRAM sooner, it will then throw away early auto-savestates. It will preserve the manual savestate.
For debugging, maybe I should print the entire replay (one line per assignment in the replay) to the screen at all times.
-- Simon