If I had to solve this problem, I would do it as follows:
c:\1> dir /b > 1.txt
c:\2> dir /b > 2.txt
This will give you the two lists of files in each folder. Now take these two lists, and upload them to your favorite unix shell. Perform a diff command to compare the two files, output it to a file. Then examine that file to see exactly which files are not shared by each folder and go from there.
It saves the manual labor involved with figuring out which file names are shared by each folder.
-Ankur