I tried to reproduce your problem, but everything works fine for me.
You have to avoid to overlap the timer interaction box with any of the quiz slide objects (bounding boxes), but that seems not to be the case.
I'm wondering if it is a consistent behavior. Which theme are you using? I see only the Submit button has been kept, which changes did you make to the master slides?
Can you try to reproduce the issue in a blank project with one question slide that you build the same way, maybe with a default theme?