That didn't happen because of the fw update. It's a long standing bug. When you remove a card and close the door the camera ignores your settings and reverts to the card that's still there. EVEN WHEN THE POWER IS OFF. You then have to go back and set all of your card settings again. If you take a card out and leave the door open, then reinsert the card, the settings will be retained.
Has anyone had Eye-Fi problems since updating their firmware?
My camera will no longer activate my Eye-Fi card when I "enable it" in the menu. It's not working but I don't know whether it's the new firmware or the card is just bad since I haven't used the Eye-fi wireless in awhile.
EDIT: Never mind, I got it working. It turns out that the firmware update changed playback of my dual cards to use the CF card which means images I lock as a flag to selective transfer via Eye-Fi wasn't getting recognized and thus the card didn't think there was any images to transfer. Changing the playback card to the Eye-Fi card fixed this.