Maybe an email to Robert might provide an answer. I've looked through various files like the ones for the UHP GUI files and through Hal's scripts but nothing out of the ordinary.
I tried enlarging the GUI window size to 200%, closed and restarted Hal.
I moved the GUI to the upper left corner, closed and restarted.
In both cases Hal's window started exactly where I left it when I closed the program.
Did you try switching monitors. I mean put Hal on the left one, close and restart to check location...or perhaps same with the right one.
Just tossing darts in the dark hoping to hit the board.