Play/pause with SetPoint/Mouse stops working after interacting with certain menus

I use a Logitech Marathon Mouse with programmable buttons (with a program called SetPoint) which I have set up to pause iTunes when I press a certain button on the mouse. It works just fine, until I interact with the Up Next, Search, or other similar style menus. Here's an example scenario that is reproduced every time I do it.

1. Open iTunes, play/pause with mouse works fine

2. Click Up Next, play/pause with mouse still works while the menu is open

3. If I close the Up Next menu, the play/pause with the mouse no longer works. Same goes for when I use the search function in iTunes.

It always used to work (pre iTunes 12.2, if I remember correctly). Now I'm on the latest versions of both SetPoint and iTunes and the problem goes as I described. I have an annoying temporary fix for the problem, since once I close and reopen iTunes play/pause works again until I use Up Next or search. However, it's a hassle to have to open and close it, and I'd rather just have a permanent solution so I can go back to pausing with my mouse buttons.