Your code is calling a Refresh action on the IManFolder, which basically means it's refreshing the metadata from the database, but not the client because the IManage API doesn't know anything about the client.
You're apparently developing a FileSite ICommand therefore you can pass a context back to the ICommand which will instruct the integrated application (Outlook) to refresh the folder view
See the post here:
http://devnet.interwoven.com/forums_vb/showpost.php?p=146198&postcount=2
I'm not sure it's a defect. I think it's by design that only FileSite is refreshed.
Either way, you should thing about submitting a bug and/or enhancement request via the Autonomy support site