I just completed a run with a real time of 37:52 (Not good, many deaths), but somehow the In Game time was a ridiculous 24:29, far better than the #1 time on here. I'll put it up if anyone wants to see it, but the run is pretty bad other than that weirdness.

Any idea why this would happen?

In-game timer ticks every "step" in the controller object, steps don't occur when paused, during messages (like getting an ability), or room transitions / loading.

Which is considered the record?

I'd say real-time (which is what the runs are all sorted by.