Are you calling common events? Given that the hamburger flickers also makes me think that you run a short common event which, by default, blocks the player from going into the pause menu, even when it's for less than a second. The hotbar simply replicates it, as you should not be able to call hotbar actions during cutscenes.
I'm turning on the switch which play autorun common event with evented animation steps, so probably I can say...yes?
BUT...
Already tested on clean project with just an event which makes "change image" for hero, and the hotbar also blinks. So looks like it's not because the commmon events (at least not only). I mean, the default burger menu also flickers during every action, which also drives me crazy ^^'