Hi Redot,
We can certainly wait for the firmware update to see if it fixes your issue as well, but I'm not optimistic.
The way the drive is handled during a Shutdown is different than during a Restart. The problem we are working on is for Restarts.
Your description is very interesting. I can't imagine why you would need to disconnect power for 30 minutes before powering up. I've never seen a board that took more than 1 minute to discharge all the capacitors on the board once the power is removed.
I encourage you to report this to ASUS. I don't have a Z87-pro board to test with, but will check around to see if we can find one.
A couple of things to try that might help us figure out what's going on:
1. Shutdown your system. Remove power for 5 minutes. Don't disconnect anything. What happens?
2. Disconnect all USB devices except keyboard/mouse before shutdown. Shutdown and see what happens (don't disconnect power).
I know you have the Samsung SSD in your system. Any other HDD's?