My question is, is there a reason for this not to work?

Details: I have two 500 Gb drives, and my motherboard RAID support, so I created a RAID1 array and booted from a Linux live medium. I then listed the disks and, apart from the obvious /dev/sda, /dev/sdb, etc. there was /dev/md126 which, I figured, was the mirrored "virtual" drive. Its size was 475 Gb; I had seen that the size of the array would be smaller than 500 Gb when I was creating it, so no surprise there. I did cfdisk /dev/md126, created the necessary partitions and chose write. It's been about half an hour now, I think. It doesn't seem like it's ever going to finish. The only thing about cfdisk in dmesg is that it's "blocked for more than 120 seconds".

Doing fdisk -l /dev/md126 in another terminal I see all three partitions I created and a note that "Partition 1 does not start on a physical sector boundary". The table is lost after reboot, though.

I tried to partition /dev/sda individually, and it worked, the table was written in about a second. The "not on a physical sector boundary" message is there, too.

EDIT: I tried fdisk on /dev/sda, then there were no messages about sector boundaries. After a reboot, I am able to use mkfs on /dev/dm126p1, etc. fdisk shows that /dev/md126 has the same partitions as /dev/sda (but /dev/sdb doesn't have any).

But at some point ("writing superblock and filesystem accounting information") mkfs is also blocked. Using it on sda1 results in a "partition is used by the system" error.

What can be the problem?

EDIT 2: I booted a freshly updated system from a pendrive and was able to create partition table and filesystems on /dev/md126 without any apparent problems. Was it an issue with the support of the hardware? My MB is Asus P9X79.