I had a similar problem with a space in the CFLAGS for Linux: Too add 'CFLAGS="\$CFLAGS -std=c99"' Matlab needs:
mex('CFLAGS="\$CFLAGS', '-std=c99"', ...
The MEX command is too smart for parsing the non-functional form, so try this:
mex('myfile.c', '-L"C:\Program', 'Files', '(x86)\lib\"', '-l l64.lib', ...
'-l cr.lib', '-l al.lib')
This looks as strange as it is. Perhaps the spaces after "-l" are a problem also. I think they should be omitted.
I'm convinced, that MEX has been grown beyond a fair level of usability: Under Windows mex -setup creates a .bat file, which is not called as batch file, but parsed and evaluated in a perl script. Actually starting a compiler is trivial and a handmade M-function would be cleaner and more stable.