Added issueCommands method.
Figured out BoxLayout error - turns out it's a common one - I was setting it as layout for the frame, while it should have been added to the contentPane. This didn't end up helping me with the layout in general though; the answer to that was that I was using the same component more than once (a blank JPanel with background color, used to hold space). Each time I added the component to another one, it was removed from the last component to which it had been added. Had to make blankTopRow1, blankTopRow2, etc. and finally got the layout working the way I'd intended.