Ctrl-L is a toggle. It sounds like what's happening is that you are bringing in a file that already has the Groove Clip metadata so it is conforming to the project tempo. When you "apply" groove clipping, you are actually undoing it so the clip goes to whatever its size would be at its native tempo.
The easiest way to tell Groove Clip status is to look at the corners. If they're rounded, it's a Groove Clip. If right angles, standard file.