This has been brought up in Blizzy's Toolbar thread first: sometimes, some MJ modules/functions can not be activated through the toolbar.

More specifically, this happens to me every time I dock two vessels. After that, most (but not all) MJ modules that I have put on the toolbar won't toggle any more. They can still be toggled through MJ's own menu, however.

Delta-V still works after docking.
Maneuver node planner, maneuver node editor, and SmartASS won't toggle until I leave the vessel for the tracking station and come back.

Blizzy claims that his toolbar doesn't care what happens to the active vessel.

I was afraid that this might be among the more lousy bug reports. Thank you very much.