Many thanks to all who offered solutions and replied to me regarding this issue, I finally got it resolved.
To summarise:
This problem occurs when the App store interrogates you computer to see if any Apps need updating, the App store uses Spotlight (the inbuilt app that tracks all of your hard drives content). the problem arises when you make clones or back ups of your main hard drive (the one that the OS runs on) Index tells the app store you have more than one OS drive and hence the app store keeps wanting to update your machine.
Solution: follow the instructions in this link,
http://reviews.cnet.com/8301-13727_7-57590306-263/tackle-a-hung-app-store-update -in-os-x/
The user Worksafe (above) kindly posted it,
1.- remove your backup drives from the Spotlight list.
2.- rebuild the spotlight index
3.- let your machine do its updates
thanks again