You could switch to send email via Plugin.
e.g. use the sendMail functions in our plugin.
And in the last months we had a few clients who got our MBS Plugin + DynaPDF + PDF/A Extension to use the optimize command and repair the PDFs made by FileMaker.
We have the same issue. We believe the 'corruption' issue is the same as no attachment. Unless we hear differently, the corrupt PDF is not complete. See how closely your situation matches this Knowledgebase writeup:
Our research, and that of others, indicates the problem is with El Capitan Mail as it happens with both FMP 13 and 14 on El Capitan but doesn't happen with 13 and 14 on Yosemite. It seems like a timing issue of some kind. We just tested with FMP 15 and seems to happen the same way.
I'd love to have someone shed more light on this as our apps output to Mail all the time. Since we need editing, a pure SMTP approach is not always practical.
You can also write an applescript to send mail, that works fine.
Otherwise the MBS plugin is maybe be a good option,