When command pod A docks with command pod B - Only Command pod A controls are accessable until undocked. I have tried and confirmed this several times. Command pod B only becomes accessable again after undocking from Command Pod A. The screenshot is a simplified example of how to test this behaviour. Try to undock and redock you will find one of the pods control options will ultimately become inaccessable.
Bug Planned Found in 0.7.3.4
Perhaps helpful in tracking down the problem by giving it a better time stamp: The ability to access command pod AG's docked or undocked was all fine in prior versions of the program - The command pod 'lock-outs' only started occurring after the original procedural landing gear update.