If you haven't done so already, I highly recommend setting this tweak in your registry, and rebooting.
It's cute when the dir command treats *.htm like *.html; it's devastating when the del command interprets *.res as *.resx.
Setting NtfsDisable8dot3NameCreation will supress the creation of shortnames for new files, but the only way I know of to remove shortname entries for existing files is to rename them.
for /r %I in (*) do @ren "%I" "%~nxI.no8dot3" && ren "%I.no8dot3" "%~nxI"
for /d /r %I in (*) do @ren "%I" "%~nxI.no8dot3" && ren "%I.no8dot3" "%~nxI"
But be careful -- only do this for data files, not for anything might be installed/registered software. Your registry is full of shortnames pointing into your ProgramFiles folder!