You have a tried a couple of the recommended methods to clear it.
Here are a couple more:
1--With the BB powered fully ON, remove the battery, hold 30 seconds, replace, reboot.
2--Change Themes and return to the present theme (Options > Themes)
3--Lastly, backup, reload the OS.
How do I reset my message counter to clear, or zero? - BlackBerryFAQ.com