Hm. Bad news Toady, seems I copied the wrong folder.
Copying the origonal save directly from .21 into .22 to try to reproduce also has the water begin flowing normally.
But copying the wrong folder may have made me identify the real problem! Yay! I have noticed something weird with the freshly copied over ramps.
Transferring the save over appears to be randomly deleting submerged ramps and stairs. And considering that there was no sign of the stairs visually where there was one previously when I was encountering the issue with the waterfall suddenly stopping, the stairs being deleted may be exactly what happened.
In the case of ramps the down ramp above it still exists, but the up ramp below vanishes.
Here's two screenshots that may explain it better. (Images are roughly 1230x708 for those with low resolutions)
So It seems to be a map conversion issue. This appears to have happened throughout the entire map, including the caverns. It is just most noticable in player made channels.
EDIT: After letting the game run for awhile I'm finding more and more ramps are getting deleted as the game continues... So it may just be 'washing away' ramps and stairs that are submerged as the game runs and NOT deleting them immediately on load. This is getting weirder and weirder.