Two possibilities occur to me. It's being stripped as part of the MIME encoding process, but if that's the case, copies you send to yourself would also have the CR stripped. Otherwise, the only thing I can think of is that a spam filter is acting on the file, but I can't see why it would strip CRs.
I'd be happy to receive a copy of the file from you and check what happens. PM me if you want to try, and I'll give you some email addresses.