Check if you Bound 'Left Click' to something. If you did you broke the Squad Command widget/UI.
If you don't have Left Click bound to something, you can:
1.Reset to Default and redo all your bindings except Left Click
2.enter /bind_save_file <filename>
open up your Live sub folder of wherever STO is located
open <filename> with a text editor (notepad works)
look for the LeftClick "" and delete it and then save the file
enter /bind_load_file <filename>
and that will restore Rally Point functionality
Had the bug for the first week and didn't realise it was just some garbage with the UI instead of an actual bug. Made a new character which didn't have the issue (and default keybinds) and more or less figured it out. I have filed a ticket for it but likely they haven't read it yet. I find it really sloppy coding practice to let a user break a UI element so easily and let them know it in one of the tickets.
Tried it the way you suggested and it still didn't work, so I just reset the "ground" keybinds back to their default values and its working now.
I have noticed, also that when saving key binds to save files (/bind_save_file) that it saves two different sets of information depending on whether you are in space or on the ground, each overwriting the previous files data.