i would just throw in another aspect: just dont play with input quantisation (personally i think its a weird feature because it is totally unnatural to play with it) since you can anyway quantize it later to your need with two clicks...
btw.. it also could be sloppy timing of your playing - do you have at least 4 clicks of metronome preroll before recording starts ?
cheers
edit: btw. if you do not use any audio (sure you will soon ;.) you could also set the metronome to "midi" instead of "audio" and disable all the latency compensation settiings...
but thats a very specific approach that brings you only trouble when you use internal instruments...