I've figured it out! When my "Max Frames per second" slider is set high (such as 90-100) I get a stutter when jumping while running, and get stuck 2-3 off the ground when standing still.
I lowered the max FPS slider to 40 and now I can jump normally as though there was no issue.
Incidentally, this also allowed my x-axis mouselook to function normally (previously it was painfully slow).
Hope this helps everyone else!
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