Odd very odd

I got a grey screen the other day and did a restore from my back up disk.
Funny thing is now my Os is running from the backup disk not the internal hard drive, why is that?

Sparse, very sparse. (your title, that is)
I don't know the answer. What did you use to do the restore? You restored files or the OS too? Or are you trying to say you reinstalled the OS? (Terminology gets in the way sometimes. You can't always be sure it's being used "correctly".)

Ok it was late, I had a long day and the iMac is annoying me.
I selected the "reinstall Os from last backup" from the menu after pressing
Cmnd+R on start up.
I did the disc utility's part first but nothing was found wrong.
This all started when safari locked up, and I then got the gray screen
and spinning wheel after restart.
This stayed like that for half an hour so I jumped onto the iPad
to see if other people had the same problem, yep they did, but
using some of the methods did not help all I kept getting was the
Grey screen.
So I reinstalled mountain lion from last backup, now it's running
from my backup disc, I know this as I turned it all off and restarted without backup disc on and the iMac goes back to a grey screen.
Switch on the backup and it all works.

So I reinstalled mountain lion from last backup, now it's running
from my backup disc, I know this as I turned it all off and restarted without backup disc on and the iMac goes back to a grey screen.
Switch on the backup and it all works.

Click to expand...

I'm assuming here that you used cloning software to do the last backup to an external hard drive? (the one you restored from) Carbon Copy Cloner or SuperDuper? Answer this question first and we'll go from there to figure out what happened.