I assume you've checked that the keys are actually moving the keys on the virtual console: if they aren't perhaps it is a problem with the midi transmission from the keyboards. You could use HW midi logging or a tool such as MidiMedic to check this. As you say some ranks are fine, then this is probably unlikely.
Does the organ have multi channel output configured? I have experienced some notes not sounding when the amps for some channels are not working. From your description, for some ranks it would appear that the sound allocation algorithm which assigns "pipes" to the C and C# "side" is being used and one of the audio outputs is not working. I suggest you might look at the configuration of the output system and check the audio hardware.
(Resetting HW's settings to "factory" conditions may reset the audio settings. You could recover them from one of the HW backups.)
Good luck.
Iain