Sorry, this is not a solution, but rather report of a similar problem, to help finding solutions! My attachments usually reach the recipients on both Macs and Windows machines (I leave the option "compatible with Windows" on although I don't know what it does). But twice now I've sent messages with attachments (always PDF) to the same iPad user, and he claims that he does not see the attachments. Yet I see the attachments in his reply!
First, I would like to know what I should do (or tell him) for my attachments to be visible on his iPad.
Second, your problem may be similar: the attachments may reach your recipients but not be visible, either because of a setting we made in Mail, or a setting the recipients have made on their machine.