Same here.

Missed this comment.
Yeah, you have to go to the checkpoints that the level has set, and if you break sequence then the checkpoints system isn't currently capable of accounting for that.

I might be able to do some things to possibly fix that in the flying mod, but that would probably cause incompatibilities with some maps that the flying mod could otherwise work on. I also am not 100% sure I could make such a fix "logically perfect".

The work-around on the user side is to stop breaking sequence. Just fly to the various checkpoint (even the silent ones) and make sure they're triggered before trying to proceed. Of course, this advice is hard to know how to do unless you more or less just use the flying mod as a way to "run really fast" and just fly close to the ground in a way where you don't go to places you couldn't otherwise walk or jump to.

You could also try filing a bug with Wolfire, but I can tell you that they're not working on the game at this time, and this bug would probably be considered fairly low priority. "if mod breaks game, stop using mod" would probably be their stance, unless you had a way to break sequence without mods that normal users might be likely to accidentally stumble into.