I use Ejukebox paired with Virtuawin to switch to and from it. If I am busy working and I want to look at ejukebox I just press a key and it switches to desktop #2 where Ejukebox is running.

I haven't used the feature in a number of months... possibly over a year so I'm not sure which version caused this to happen but with the newest version up now if I have song popups turned on (the small square that comes in on the lower right side), it steals the focus and brings ejukebox to the screen despite the fact that I was working on a different desktop than the one that ejukebox resides on. I have a hotkey for next song as well and on the older versions I remember the popup would display on top of my desktop even though it should not have since I wasn't currently on the desktop that ejukebox was started on, but it didn't bother me, I kind of liked that as a feature actually.

I'm not entirely sure where the "problem" lies, either with virtuawin's window management or ejukeboxes approach at creating the popup... But maybe you could investigate it because it is definitely an incompatibility between the two programs. Perhaps Ejukebox accesses the video hardware differently (directly?) on this newer version? I seem to remember one of your changelogs mentioned a change as to how the graphics are rendered, possibly that could be when this issue surfaced.

on regular single monitor single desktop scenarios v5 keeps the interface in the background on pop-out. to fix your setups issue i think you could right click on the album art in the popup and check Pin on the menu. and/or minimize eJukebox