In my test environment, I'm using the latest version of the plugin (20 Aug 2011) in 0.6-beta. I'm seeing an issue I've seen for quite some time with spinning progress wheel during a "mark message" operation. Can anyone else duplicate this? Here are the steps:
Go to any folder with multiple unread messages. Close the Preview Pane if you use it.
Open one message to view it.
While the message is open, right-click the folder that contains the open message, and select "mark all as read".
In my experience, the progress wheel will drop and spin ("markingmessage"), but it never refreshes the folder list, and the dialog never goes away. You need to click into a different folder to escape the hang, at which point all the messages will have been marked as you requested.