It's a known issue that Amavisd doesn't read its own whitelists for checking bad-header.

Known issue for Amavisd.

Possible solutions:

1) disable bad-header check in Amavisd.
2) Wait for upcoming iRedAdmin-Pro release, it allows admin to manage global, per-domain, per-user spam policy, including a new option: "Bypass bad-header email".

For option 2), if you cannot wait, please try steps below with the latest iRedAdmin-Pro:

*) Go to global spam policy page: System -> Anti Spam -> Global Spam Policy.
*) Change some setting to trigger iRedAdmin-Pro to create required SQL records in SQL table `amavisd.policy`.
*) Now login to SQL server as either `root` or `amavisd` SQL user, find record in sql table `amavisd.policy` which has 'policy_name=@.':

sql> SELECT * FROM policy WHERE policy_name='@.';

*) Update its columns:

sql> UPDATE policy SET bad_header_lover='Y', bad_header_quarantine_to=NULL WHERE policy_name='@.';

That's it.

Notes:

*) if you changed any setting in Global Spam Policy after above change, values of column `bad_header_lover` and `bad_header_quarantine_to` will be reset (because the latest iRedAdmin-Pro doesn't handle them).
*) If you just want to disable bad-header check for emails sent to one local domain, please go to domain profile page, tab "Spam Policy" instead of global spam policy.

Let me know whether it works for you or not.