Do you have cats? or other critters in your garage? LOL I found cat hair(I hope) on my seats and carpet. Male cats are know to mark their territory(spray) even if fixed sometimes(luckily not in my car).
I should have set the alarm.
Other than that i would think, logically, that it would be better all around to leave it down. Just make sure the window doesnt bend the wrong way when you lower it. You might have to stop and help it a couple times.
