Hi Ben,
Lets say I have a drum track playing a standard 4 beat per measure with the kick drum on the 1, 2, 3, and 4. If I then record a separate bass track and mirror the kick (one note on the 1, 2, 3, and 4), it all sounds great to the ears while I am playing. However, when I go back and listen to it and view it on the screen, the bass track is about a half beat behind the kick drum.
I should note that prior to updating my OS to El Capitan, I did not have this gap.
Thanks, Kevin