Sorry Karrthus for my somewhat mean comment. I saw that you're level 51 so I guessed you must know what you're talking about. I tried looking at your automated piston door, as it follows the same detection system.
The problem was my setup. Apparently when you have a repeater in front of a comparator, and you have a command block right in front of that repeater, the comparator stays active after the command block finds the player.
Basically I'm using a setup, that I found on the internet somewhere, that has a checking command block, going to a /tellraw command block, which sends a signal that stops a clock.
I should thank you, since if you didn't reply I would never check your profile and never would've found the solution. xD
So thanks.