What do you mean invalid? & what do yo mean by email certificate ?
if the cert is an attachment and was not flagged as a virus, I don' t see how a simple fortigate is going to invalidate it. If you using a mail gateway and tls/ssl encryption, same here, the firewall and with no-ssl inspection , is not going to mangle your certificate.
Other questions & ideals;
Do yo have any UTM features enabled?
If yes, can you place a specific fwpolicy for that host with no UTM security profiles enabled and re-test?
Is the cert a x509 formated certificate & some type of attachment ?
If yes, down the cert before and after sending and read it back in using, does the 2 cert matches?
openssl x509 -in " download cert name attachment or whatever" -text -noout
You need to provide more details.