Well, two things: One, remember what files are on the OptFS - Only supporting files. Those files probably did get copied, but until you copy the rootfs, you can't access any applications, as the application excecutables(or, if they are stored on thw OptFS, any links to those files) aren't on the RootFS.

In Windows terminology, its like copying your old programs to the program files directory, then wondering why those programs aren't showing up in the start menu.

Edit:
Also, I've gotten that "can't flash" message - Flashing to PR1.2, and then immediately flashing the rootfs with the flasher tool seems to fix that - IF your RootFS backup is not corrupt.

I am thinking though that bad blocks have some part in this whole thing - thats why some of us can backup and restore successfully, yet others do the exact same steps and it not work quite.

If you can't flash, hold on for a while, see if you can't get that ubifs mount code working, and I'm gonna try to figure out a different way of backing up and restoring that is more tollerant of bad blocks.