[Solved] No reboot/shutdown

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?

Quote from lrusak

Test a clean install, then report back

Obviously clean install works, but I would like to pinpoint the issue. Some time ago I tried to disable addons one by one and different PSU-s with no luck.

Now I found out that HDD keeps spinning after a soft reboot/shutdown, network LED keeps flashing (but there is no connection) and the activity LED keeps flashing. Maybe something still needs the network when it's already down and prevents the shutdown?

Edit: I think I found the problem finally. After some heavy trial and error I can say it's the swap partition that prevents the shutdown. Guess the swap isn't needed anyway as much as I thought one day.