I've had this conversation in email with a few people so I thought I'd have it with everyone. Even if you don't use the SSO functions provided in BizTalk Server your BizTalk Server is still using SSO. Ok, so that sounds a little counter-intuitive but here's why it isn't:
The SSO functions encrypt important information (like usernames and passwords) securely in the SSO database. It turns out this storing of information securely in an encrypted database is useful for lots of things that shouldn't be in plain text in the database. Indeed BizTalk Server persists the adapter configuration information into the SSO database so that the URI you are receiving from or posting to is not persisted in plain-text in the open. Hence the Explorer object model (and therefore the BizTalk Explorer tool) is going against the SSO service and database to receive information. As a result if SSO isn't running, or if it isn't "properly setup" you will get SSO errors eventhough you aren't using SSO at the user level - because we are.
Hopefully that clears it up for everyone.