After upgrading to El Capitan beta 5, 10.11 Beta (15A235d), Apple Mail 9.0 (3073) is not remembering any SMTP accounts for non-iCloud accounts. For example, I have gmail and other IMAP mail servers. Mail forgot all my SMTP servers after the upgrade to beta 5; and adding the SMTP server then going back into the Outgoing Mail Server setup shows the SMTP server you just added was not saved. When trying to send an email with a missing SMTP account, you can add the SMTP server and the single email gets set OK, *but* that SMTP server you just added is not saved after sending that single email.
The SMTP server for iCloud accounts is saved and used without any problems.
This problem did not occur in previous El Capitan betas.
reported to Apple; radar #22026537