I loaded a song created in BIAB, the tracks generated correctly, but...

• The metronome count-in on the first two bars plays, but on the off-beat instead of on the beat,
• The metronome does not stop after the two bar count-in, but continues through the song, still on the off-beat.
  

In the metronome settings, "Metronome shut-off after count-in" is checked. How can I sync the metronome to the beat and get it to shut off when the song starts?

FWIW I think the metronome uses the default windows synth. I know of no way to change this. You may be hearing latency compared to other tracks (?)

Certain features work that way, and for me the metronome is one.

I have a click.mid file I use.
It's four bars of sidestick in MIDI.
I just copy/put it in at the Tempo and Bars I need (there is a 'Fill' option if you want to put it thru the whole song quickly), then render it to audio.
Once it's Audio I can make it as loud as I want .. like for that drummer who needs it the most.

Also, there is a new Click Track feature; are you sure it is metronome and not click?
Turn Metronome off and test.

It was the metronome I was hearing, so I created a MIDI click track to see how that would work... same result - the clicks were not on the beat.
So your first suggestion was correct - it was a latency issue. I used the latency adjust feature in the MIDI driver setup, and all is well!
Thanks for your suggestion - I should have thought of that, but you helped connect the dots.

Good job finding it and fixing it, and thanks for letting others know a possible fix in the future