Try the following:
1) Delete the offending DLL from your Program Files\Common
  Files\System folder and subfolders.  You will notice
  that the Windows File Protection mechanism will
  immediately replace the file you have just deleted,
  hopefully with the right version of the DLL

2) Run your VS6 installation again

If you are still having problems, do the following:
3) Rename the offending DLL found in %SystemRoot%\System32
  \DllCache

4) Search on your hard drive for the latest version of the
  offending DLL. You should find the latest DLL typically
  in any Service Pack, HotFix or Windows Update folder,
  if you had selected to save these files when you last
  updated.  If you do not find the latest DLL, proceed to
  the next step

5) If you found the latest DLL in the previous step, copy
  it to the DLLCache folder

6) Reboot your machine

7) Repeat Steps 1 and 2 from above.  If you did not find a
  replacement DLL from Step 4, you will be prompted to
  insert your Windows CD-ROM

Of course, you will need to be logged on as a user with
local administrator privileges on your machine to perform
the above procedure.

Hope this helps