I'm using the Palm Threaded app with rlToday (see the Themes section) and it only has "Go to" (left key) and "Dismiss" (left key) as options.
When I hit "Dismiss" the notification stops and my counter for rlToday resets to zero instantly.
The SMS stays as unread in the Inbox.
So that's one setup to avoid this but I'm not sure about using the default SMS program with the Messaging plugin. I forgot what the default behavior is.
I wonder if a force-screen refresh would reset the counter e.g. go to Settings --> Today and select/unselect a random plugin, then hit "OK" and see the Today Screen refresh itself.
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