Go to Options > Advanced > Applications and scroll the Messenger application and don't click on it, just scroll to it. Click Menu > Delete and remove the application.
Now, do a reboot: With the BlackBerry device powered ON, remove the battery a few seconds and then reinsert the battery to reboot.
Finally, use your BlackBerry browser to go to BlackBerry Messenger
and download/install the Messenger application again.
After installation and possibly another reboot, check your Instant Messaging Folder, or Downloads folder for the application.