I have set up a new mailbox as I've done countless times and for some reason none of the emails i'm putting into it are being stored there. It keeps indicating zero messages when I click on the mailbox and I have no idea where the emails went.

Sorry but can not duplicate this issue on any of the 3 Apple Computers running Monterey 12.6.

1 - Restart in Safe Mode. This will perform a Disk Repair, clear cache files and only load Apple Software, extensions and fonts. The boot up will be slow and can take some time - Normal.

2 - Does the issue present in this mode ?

3 - Sometimes a Safe Boot followed by a Normal Boot will just put things right.

4 - If not - there could be something in the main User Account playing up. To further isolate this - Set up users, guests, and groups on Mac. Then log out of the Main User account and log into the dummy account and test again if the issue persists.

5 - If the issue is present in the dummy account - then, this appears to be a System Wide issue on the computer.

6 - If after performing each of the above steps in the order that have been presents and still have issues - please advise for possible further assistance.

Organize email on your Mac - Apple Support