When I set an account to act as a catch-all account, the sorting rules only apply to emails addressed to the specific account.
e.g. username@domain.com emails get handled by the rules, but another@domain.com emails are being ignored by the ruleset. Both sets of emails are still being delivered correctly, it is just that some are not being handled by the ruleset.
If anyone understands my situation, and knows how to resolve it, that would be fantastic. I am more than ready to be told that I have missed something obvious.
