Disguises aren't guaranteed even when your back is turned. If a guard stays in the same room as you for a long time and gets a good look at you, he'll raise the alarm anyway.
Also, I think they'll raise the alarm if you leave desks, safes, and doors open (maybe only if you do it a lot?), since I've seen the alarm go off even when nobody's in the room with me. I do know that the guards will follow you if you leave doors open behind you when they're chasing you. Close the doors behind you and you can shake them off.
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