Ya tbh I have no idea what I did that fixed my issue, I had a launch of probes, all of which had partial control even though they had 100% signal and probe cores were on. After copying a lot of game files into an external folder, overwriting my save, then reloading the original save just after docking with the space station then all of the probe cores were hibernating. Went into my VAB and checked the probes in the subassembly, hibernation on, checked the vessel I originally put them into the subassembly from and the probe was not hibernating. No idea how it was caused or resolved. So didn't feel it contained valuable enough information for anyone looking for a resolution to a similar issue.
