The Hubin compensated throttle setting is for non-governing ESCs: it increases the throttle as the flight goes on to compensate for battery sag.
The ESC governor setting is for non-compensated throttle settings (actually, it's for helicopters, but don't tell anyone here that).
Put the two together, and you're going to get a setup that speeds up as the flight progresses. So -- turn the throttle compensation off, and use governor mode.
As to the motor, the clackity-clack you heard is not good. Without the speed increase to confound things, you can just look for why a motor would clack and stop. Loose anything would do it -- it could have been a loose magnet, or a loose prop, or anything.
I would probe the motor for loose magnets, myself. I would go over the motor carefully for loose anything. If there's an angle that you can look at the motor and see all the magnets inspect for one or more out of place. If the motor passes that test, see if you can stick a toothpick or other similar tool into the motor and push each magnet around -- if it wiggles, then Mark's suspicions are well founded. Try wiggling the magnet housing (the part that spins) -- it should be tight on the bell, and the bell should be tight on the shaft. The shaft should rotate smoothly on the motor base, without excessive end play.
Clattering may have also been caused by one phase of the three coming loose. So, get an ohm meter and check continuity between each pair of motor wires. Don't just do this once -- do it while you're gently tugging on the wires, pushing on wires, bending the wires, and otherwise giving any intermittent open circuits a chance to pull apart.
If you don't find any out-of-place wigglies, I'd strongly suggest that before you fly the critter you run it at full speed on the ground and make sure that everything is tight. If it is -- shrug, cross your fingers, and go fly.