Yep, it's just the way the server is configured:
Let's say personal namespace is "INBOX" and shared namespace is "SHARED", the actual folders would then be:
Inbox <<-- the folder, not the namespace
INBOX <<-- the namespace
Sent
Drafts
Deleted
Archives
SHARED
Sales
Marketing
And Aqua was only asking the server for folders under "INBOX".
With the namespace forced to "none", Aqua is now asking for all folders, and that includes everything under "SHARED".