windbg -rtl %windir%\system32\autochk.exe worked and was able to debug
the autochk native application (i.e. app that uses the native API NOT
the Win32 API that can run on BootExecute).
cdb -? says this about this option:
"-rtl uses RtlCreateUserProcess instead of Win32 CreateProcess"
So if debugging your native application works with this option you may
be able to launch it with RtlCreateUserProcess.