Currenlty, when you 'hide' a window using the left-most default button in the upper right corner of a window the window 'hides' as a button at the bottom of the Regulus desktop. It's a bit add to have this since the button also exists in the tray, and the visual effect is that it looks like you have 2 trays.
The ideal fix (I don't know how possible this is though) would be to make it 'hide' into the Regulus tray directly, rather than using the default version of the hide. If this doesn't work, then I'd almost be tempted to take out the 'hide' option entirely.
But, I'm really not sure what the best thing to do is.