Does this issue manifest itself when you have the phone plugged in? Can you get a logcat of the issue? Throwing things at the wall and seeing what sticks may not be the best resolution here. There are ways of finding out the underlying cause.
mpdecision is not the cause here (That only affects the secondary core) nor is min frequency (You can override it in the HypnoToad images too, just set another governor (like say 'conservative). In FatToad it may look like it resets because Cyanogenmod doesn't display the second core in the performance settings, but changing it is sufficient for testing. The official CM 11 builds do not have the touch boost (which only affects things after the phone is awake, and merely sets the secondary core's frequency up to 1184 Mhz when you are touching the screen, but the affect on the percieved performance of the phone due to this is immense)
Deep sleep is likely closer to the main cause because that affects both cores, and if the system isn't receiving the proper signals to wake back up, this can happen. Throughout development on apexqtmo, we've run into similar problems, and it's always helped by getting proper documentation from those who are experiencing the issues.
TL;DR: Trying random things likely won't solve this issue. Getting all the information you can will help.
TeamApexQ -- irc.freenode.net/#apexqtmo