Have done some more testing on this issue and have found that if there is more than one HDD on the system then to prevent the occurence of:-
"This version of System Recovery Options is not compatible with the version of windows you are trying to repair. Try using a recovery disc that is compatible with this version of windows."
the windows system disc has to be on a lower channel than any other disc and must be the first disc in the boot priority list
all discs but the system disc should be disabled in the BIOS