I had the sort of the opposite configuration in place. nnimap was my
primary select method. Making nnimap my secondary select method seems
to have stopped it from making *eveything* in my IMAP folder as read;
however, now nothing is being marked as read after I read the mail message.
For posterity, here's all my gnus-affecting settings:
(custom-set-variables
'(send-mail-function (quote smtpmail-send-it))
'(smtpmail-smtp-server "
smtpcorp.com")
'(smtpmail-smtp-service 2525))
(setq user-mail-address "
co...@corbe.net")
(setq user-full-name "Daniel Corbe")
(setq gnus-select-method
'(nntp "
us.news.astraweb.com"))
(setq gnus-secondary-select-methods
'((nnimap "
apollo.corbe.net"
(nnimap-address "
apollo.corbe.net")
(nnimap-authenticator login)
(nnimap-server-port 1143)
(nnimap-stream network)
(nnimap-expunge-on-close 'never))))
(setq gnus-mime-display-multipart-related-as-mixed nil)
(setq mm-text-html-renderer 'w3m)
(setq mm-inline-text-html-with-images t)
(setq mm-inline-text-html-with-w3m-keymap nil)