Some time ago you added the following backfill patch: https://sourceforge.net/p/vpopmail/patches/86/
The problem is that it erroneously considers a mailbox to be in a hash directory if the mailbox name is contained anywhere in the domain storage path. Let's consider the following domain storage file path:
/home/vpopmail/domains/jaro.user
The following mailbox names will trigger the problem:
pma
pm
mail
...
I've attached a patch which fixes the bug.
Here is an example which demostrates the problem:
The expected storage directory for the mailbox "test123" is "/home/vpopmail/domains/jaro.user/test123", not "/home/vpopmail/domains/jaro.user/pma/test123"