My colleague installed a RHL71 system with two disks, and converted all 3
partitions to software raid after the installation, including root (there
was no separate /boot).

There was LABEL=/ in /etc/fstab.  Label in /dev/sd{a,b}1 and /dev/md0 was
"/" for all of these.
  
mkinitrd greps for /dev/md in /etc/fstab and if not found, doesn't enable
raid modules in initrd.  Thus, if you have only LABEL's in /etc/fstab,
you're in for a surprise as raid modules aren't enabled if you don't run 
mkinitrd -v.

Second problem is probably not mkinitrd's fault but if there's some
connection:

However, even if you run mkinitd --with raid1, and the module gets added,
when you boot raid1 module gets loaded but the partitions won't be
autodetected and mounting root fails (the classic 09:00 error).