Nate, that fixed it. I usually use Alt-Tab to switch to different windows. Hotkeys appear to stop working in Spine when I switch back. When this happens, if I briefly press the Alt key, all Hotkeys appear to start working again.
If I go to another window and back to Spine just using the mouse and lazy focus, the Hotkeys work fine.
So modifier keys not being released correctly appears to be the issue and pressing the modifier keys seems like a good temporary workaround. Thanks!