I love Message Alert and been using it for many years...
But that might be one of the product short coming... The program doesn't "sense" if it is in the holster or not. But you can select the option of "Tone" or "Vibrate/Tone" if you want to make sure it vibrates... The only drawback to this is that your Blackberry will vibrate even out of the holster.... Maybe in the next version?
In the meantime, this is the only product (that I know of) that trully supports "Repeat Notifications" and that will Alert you at a user selectable intervale until you shut off the alert... To me that is priceless... I never miss an important message.!
Good luck... And by the way... The support team is pretty good overthere... I would expect you will get an answer to your question today.