So say you have loop recording set up. Say you have guitar/bass with an amp sim set up.
If you hit record with the cursor at the beginning of the loop point, with a two-bar count in, the plug/signal disappears and fades in at that point. VERY distracting when doing takes.
Back in the day, when I used to use reaper, I don't remember that happening.
I/O settings and manual don't help. The metronome seems to be tied to your soundcard output, is that correct?