> However, what can I do about the secondaries? Anything?

Secondary or foreign servers should work if you give a fully qualified
group name; at least it works for me with a nnimap server in the
secondary select methods. Also, 'read' marks in Gnus should directly
correspond to the SEEN flags on the IMAP server. If you activate the
IMAP logging, you should see stuff like

595 UID STORE 2987 +FLAGS (\Seen)

when you mark message as read (and -FLAGS if you remove the marks on a
message)

-David