Given what you have told me, you are using calibre's content server to transfer books, and you are not using a calibre release that puts custom fields in the OPF. As you are seeing custom field information (fields that you created), that implies very strongly that stanza is getting its information from the content server.
The attached screenshot shows what Stanza will see for a book in my library. Calibre's content server currently publishes to stanza (or anyone else using the OPDF version, as stanza does) all non-empty custom fields. As you can see, calibre is sending comma-separated lists for all multiple fields, including tags. I infer from your comments that stanza would not show all the tags. That sounds like a stanza bug.
The only thing I can do is change calibre to allow you to limit what fields are sent to stanza via the content server. I certainly cannot change what stanza does with the information.
EDIT: Cross posting bites again! You are welcome! Nice cat, too.
