How to reproduce:
at this point you can see that freeplane does not recognize the transparency status, and the button is not toggled although it is already transparent.
and now, pressing it again to make it transparent toggles the button but makes it black color..
I can confirm this behaviour but only for Node Background and only in case of no initial color (blank value).
If the initial color is set, Make Transparent work OK for me.
I think that is because of the setup on View -> View settings -> Rectangular selection. If Rectangular selection is checked, the background colour keeps transparent when the node is selected. Otherwise the node selection style overrides it.
Preview 1.9.13_18