I had the same problem. I tried running OBS studio as administrator, and also making sure "Never disable hotkeys" was selected under Hotkeys Focus Behavior in Advanced settings of OBS. I was getting this weird behavior that my macro keys would work *sometimes* (the worst behavior there is). I found a crude workaround here.
What I did was program my macro pad to switch to the OBS window, press the hotkeys, then switch back to my application (PowerPoint slides in my case). The commands looked like this:
Windows Button+7 (this switches away from the OBS window, so that the next command doesn't minimize it)
Windows Button+8 (this switches to the 8th window in the taskbar, my OBS application)
My hot key goes here (Ctrl+Alt+whatever)
Alt+Tab (this switches back to whatever I was working on in PowerPoint)
I used 0.1 sec delays between each keystroke.
This was very annoying, but this sequence is effective. Switch to OBS, do your stuff, then switch back. Also, it assumes my taskbar programs need to stay where they are. If I rearrange them, I would need to change those numbers in front of the Windows Button.
I also have a G600 Logitech mouse that doesn't suffer from this problem. The hotkeys just work in all windows regardless.