I've encountered this problem on 2 separate systems with separate email accounts and have not been able to fix it other than by switching to AirMail 2.
After upgrading the computers to El Capitan, mail will occasionally not be able to load any content in messages. Screenshot:
This doesn't happen 100% of the time, but when it does, it essentially renders mail useless. It happens with emails in the IMAP account (just a standard Rackspace IMAP account here) and emails that are saved in folders "On My Mac". I've done pretty much everything under the sun on this. Safe mode. Rebuild. Re-index. Delete the entire Mail folder from library and re-import from backup. Clear font caches. Reinstall El Cap. Even start a new user account and pull in the IMAP account fresh. Systems are on 11.11.4. It's maddening. Anything I can do to not have to spend $9.99 a client on AirMail, and stay within the Apple ecosystem? Anyone else have any success resolving this issue?
Seems to be the same problem as this: Blank emails in El Capitan Mail.app But that remains unresolved as well.