I'm sorry I probably didn't express myself very well. What (in my opinion) is happening is that when you launch a game, Cortex automatically terminates the CCleaner process (the one running in the background) and when the game has finished, Cortex launches CCleaner process again. The problem is that for the latter it doesn't use correct arguments, which leads to opening the main CCleaner window instead of just running CCleaner in the background. So, if all this is a valid theory, there should be two ways out of it, both trying to prevent Cortex from terminating and restoring CCleaner:
Add CCleaner as an exception to Cortex, so that Cortex optimization will skip it. The exception you added would prevent CCleaner from cleaning Cortex installation folder (which it doesn't anyway). This is not what we need. We need to ask Cortex to stop optimizing CCleaner, so the exception needs to go to the Cortex application.
Prevent CCleaner from running in the background. This in your case will probably mean switching off automatic updates (in Options -> Updates). If you don't have automatic updates on, then my whole theory is probably invalid.
The first solution is arguably preferable. :)
Edit: It seems that what you need to do is untick CCleaner in the Game Booster window