Here is my full modlist from CKAN. I was able to workaround the problem by commenting out the lowPowerMode() function in the cls.ks script. Force stopping CLS does not allow me to exit Hibernation. As for what mod or difficulty setting removed the ability to toggle hibernation, that I'm not sure of. I'm currently trying to figure that out. For some reason though, the functionality is still there, just not accessible to the player. So CLS was able to set the command state to Hibernation, with no way to bring it back to Operational. I will look into this further and see what I come up with. I understand if this issue is unique and therefore outside the scope of CLS, especially since I'm not sure yet what removed the ability to toggle Hibernation in the first place.
Edit:
It's Kerbalism that removes the ability to control the Command State of the probe. It handles that different using its own scripting. I just tested it using a Stock save with only kOS, and Kerbalism.