@LoudLemur I think for admin the TOTP has to be set in the ini file (https://github.com/the-djmaze/snappymail/issues/84#issuecomment-885181768) . For users, the 2FA extension is used.
The 2fa is shown in admin login page, all the time for me as well.
But if you can identify the bug, maybe you can report this upstream since 2FA auth comes from snappy and not from Cloudron.