Have you enabled "Show hidden/system files"
Other than that, you can do a comparision of the individual directories right click and go to properties ( I assume that the back-up drive is suppose to contain what is on your Main drive. If everything you want is on your main drive and you cannot find the discrepency, the just reformat your Back-up drive and start over. KEY WORD HERE IS, their is nothing you need/want on the back up drive.
Added: then there is the hard way - go to dos prompt, do a cd.. untill you are at the root directory (ie c;\) then type without quotes "Dir *.* /s > list.txt" do this also for your back-up drive. Then print these two files and over a beer (may need a keg) compare the two lists.