AFAIK, this is a limitation of Notes IMAP
It's been quite some time since I last
tried to set up IMAP Offline in a Notes Client. As far as I can remember,
I never succeeded in sync'ing anything but the Inbox. IMAP Online, on the
other hand, isn't a good alternative, since it doesn't (of course) give
you offline access to mail, while any state-of-the-art Web mail UI provides
a much better user experience than Notes IMAP Online.
Notes IMAP (not to be confused with Domino IMAP) never received much attention
-- neither from IBM, nor from the user community. It's a "dead"
feature IMHO.