I switched the command module I was using, and I never had any passenger compartments on my vehicle, but im still getting that problem of "limited probe control", I even have a pilot onboard my command module. Also, what I mean by limited probe control is, I cannot fine-tune my throttle, and I cannot steer without using SAS or MechJeb, so basically I cannot manually control my craft.
Edit: Im even having this "limited probe control" problem on the launch pad, also I have enough electricity as well.
Edit 2: One more thing I forgot to mention is I am indeed in a COMMAND module, not in a passenger module.