Hi Leo,
Last week, I also opened a case by Symantec for an OWA issue we have at one our customers.
During the troubleshooting, the Symantec engineer told me that, when working with multible mailbox stores, the Backend2003setup script should be run for every existing mailstore on the server. Otherwise only users in the default 'Mailbox store' will have the OWA functionality. Of course, this means that the wsf script needs to be run manually with specific parameters, like :
"cscript backend2003setup.wsf /formregmbx:SystemMailbox(1234-12234-87652833)"
=> the number is just an example, you must use the real hex number of the different SystemMailboxes you have.
This is just a hint from my side. To be sure, just open a case at Symantec. They have all information about this.
Cheers,
Rudy