Comment 3 for bug 745800

Yes, this does appear to be the result of bug 733240. Rebooting got the filesystems clean again and os-prober found the OS in the extended partition.
I'll mark this as a duplicate.
The reason for the unclean unmounting was from the rescue CD, however, after changing the root filesystem multiple times. This is a separate issue. I did originall also install grub from withing both OSes, not just from the rescue mode alone. So the filesystems were left uncleanly mounted, somehow.