Choose an instrument, make a new pattern, open the piano roll, hit the little button for the countoff and record by toggling the record button and hitting play. Afterwards, you can quantise (start times for example) from the dropdown menu in the piano roll.
It's kinda weird i can't help. I never used FL studio just because back in the days when it was called fruity loops most producers disliked it. But nowadays it's on the top of the list i gotta say the top is deserved for fruity loops life long free updates when purchased. But it shouldn't be hard to fix the issue you have there.
I never liked the way MIDI is recorded. (Neither on hardware)
I usually want the keys that i'm playing to be recorded but i want them all to be the same velocity/release. (Usually velocity 78%, which is the standard velocity in FL)
I wish there was a MIDI-Keyboard that had lights underneath they keys. So you can light up the notes that are used in your scale/and turn off the keys that aren't used in your song)