Gmail not working in Smart Mailbox when iCloud Account is activated

I'm using Mac OS 10.11.1 on an iMac 27" (2011)

I use Apple Mail as a mail client and I have set up several Smart Mailboxes to show certain messages from some of the mail accounts i use.

The accounts I use:

1 icloud account

1 Exchange account

2 Gmail-Accounts

The Smart Mailboxes are set up to show mail from exchange, icloud and one of the gmail accounts.

And here's what happens:

When i upgraded to 10.11., mails from my gmail account were no longer shown inside the smart mailbox.

I checked the settings: Instead of my gmail account, mail had selected the icloud account a second time. I changed it back to gmail an closed the settings. I opened them again and the setting was changed back to icloud.

Long story short: The only way to show my gmail account in a smart folder is to deactivate the icloud-account in apple mail (which is not really an option).

This seems to be a real bug.