I finally had time to look into this further and see what is going on. When the conversion tool runs, it is placing all IMail MailBox folders directly in to the
/SmarterMail/Domains/Domain.com/Users/john.doe folder
instead of in the
/SmarterMail/Domains/Domain.com/Users/john.doe/Mail folder
seems like an EASY fix that ST could do on the tool to make it work right.
I have tested moving the IMail mailbox folders into the MAIL folder of a user, STOP and START SMail service and the inbox shows up fine. Any other folders just need to be added by the SMail Web GUI and the message inside show up right away.
But for my last bit of migration today, it's easier to just do an IMAP migration on the 150 mailboxes or so