Even though you're working under Cygwin, I'd be careful with how you're capitalizing your filenames. Try ensuring that you're using a ".s" extension instead of a ".S"
If you're still having a problem, drop down to the commandline and try running make for your kernel but add on "V=1" to your commandline arguments to make. This will force verbose output to be on (which will show each command being run).
If you're having problems running from the commandline, let me know and I'll post the commands that you need here in the forum.