Q: smart mailbox problem with El Capitan

You say you have two Gmail accounts. Do you have the same problem with both of them?

Please delete the problem account in the Internet Accounts preference pane, then recreate it with the same settings. Quit and relaunch Mail. Test.

Oddly enough, I am also having a problem with one of my smart mailboxes. I have one iCloud mail account, and three GMail accounts. I have smart mailboxes for each GMail account to display only today's mail. Each of the smart mailboxes use the following filters (messages must match all conditions) for each account:

1. Date received | is today

2. Message is in mailbox | <name of mailbox> (All Mail)

If I set the 2nd condition so that it names the very first GMail account I added to Mail, then click OK, the mailbox name reverts back to "No mailbox selected". Again, this only happens with the very first mail account I set up in Mail. The other two GMail smart mailboxes work as expected.

I've tried deleting and recreating all mail accounts, and some of Linc's suggestions, but nothing has worked.

EDIT

If I untick "Enable this account" for my iCloud account in Mail preferences then all of my smart mailboxes work as expected.

EDIT

 

If I untick "Enable this account" for my iCloud account in Mail preferences then all of my smart mailboxes work as expected.

That works for me too! Not an ideal solution, but a good enough workaround for now (especially since I really don't use iCloud email).

In fact, when I disabled iCloud, all of my smart mailboxes corrected - either instantly or once I selected them. In other words, I didn't have to re-edit their settings to correctly select the Gmail mailbox... they just kind of reset automatically.

As an aside - I'm following a few threads on this same issue. In this one, user "jkroening" had multiple Gmail accounts, but also only issues with one of them. He suggested it was due to it being the same email associated with his iCloud account. That strikes me as a red herring, but maybe not. I have only one Gmail account, so cannot confirm, but it is the email associated with my iCloud account.

In any case, thanks for the tip on disabling iCloud. This has been driving me nuts!

Had the exact same problem.  The Gmail account I use for iCloud login wouldn't stay selected in Smart Mailboxes (folders I selected from that account would be removed if I closed the Edit Smart Mailbox dialog and reopened).  No messages would be selected from the folders I selected.

As soon as I deselected iCloud as an email source, Smart Mailboxes started working properly.

This problem DID NOT affect the Gmail account that had a different name than my iCloud account.