Whoa, an interesting bug. I'm forwarding this to the Cygwin mailing list for reference. I might take a deeper look over the weekend if no-one beats me to it.
It seems like running batch files (.bat, .cmd) inside a directory with an at sign and a space (such as '@ x' or 'x @') fails. /w/temp/@ x$ ./hello.bat 'W:\temp\@' is not recognized as an internal or external command, operable program or batch file. -- David Macek
smime.p7s
Description: S/MIME Cryptographic Signature