How is the command being run? From a process or from a command line?
Make sure the command is being run from a 64-bit process (or a 64-bit cmd.exe console window). Otherwise, the %windir%\System32\regsvr32.exe
command will be redirected to %windir%\SysWoW64\regsvr32.exe
and a 32-bit regsrv32 will be run (which can't register 64-bit DLLs).
You could also try using %windir%\sysnative\regsvr32.exe
which will redirect to the real %windir%\System32\
directory (but only from a 32-bit process, so if you use that take care to make sure no one tries to run the command from a 64-bit process).
See File System Redirector on MSDN for details.