I'm not sure if this is what happens but it's happened to me 3 times so far. When riding in 2nd gear and I go to hit the back brake hard the bike seems to drop down into neutral and it makes that grinding noise like I'm trying to shift into 1st to soon.
Maybe its just my imagination or maybe I'm kicking the shifter down without knowing. Not sure.

When you get on your brakes hard and your tire start slipping/skipping, you are essentially rocking your secondary shaft back and forth. I do the same thing at times while stopping hard but my gear doesnt go to nuetral (maybe because I'm never in 2nd when this happens). It's because the back tire ever so slightly skips on the ground causing the wheel to move then stop, move then stop, move then stop.

Do you hear a constant clunking sound from the trans at all before it slips out?

Sounds like your second gear is failing. Mine shattered and I had to rebuild the trans.