Your install would have the boot info on the boot drive as well as the second drive and since it takes both to boot, you can see what happened.
Why not install again after you have the hard drives arranged the way you like?
Ok i installed linux ubuntu to my backup harddrive. Used wubi. My intention was to take out the orginal harddrive cause it was only 40gb and swap it out for the 2nd harddrive. cause it was 250gb. when took out the 40 and put in only the 250 i get the c:/bootmgr error. if i put the 40 and 250gb in i get both boot options. did i install ubuntu wrong? is there away to install it ona back up drive and have it as the only boot option or does it only work if there is a windows hdd present?