This issue has been around for ages now and I never got an answer in OE forums. This was even around with RPi 1 and is still present with RPi 2, so can't be hardware related.
Problem: Reboot and shutdown aren't working completely. System starts to shut down, screen goes black, network goes down, but the Pi itself doesn't reboot or shut down completely. Just like there is something keeping Pi from shutting down. Searching logs won't help, as everything is normal there.
Only way to reboot completely by software, is "reboot -f" but that's almost the same as just cutting the power.
What could cause this issue or is there any way to debug it?