Can't help you with your missing data, but I just did rough estimate on mine and it adds up pretty well to the totals showed, but I'm nowhere near your totals. The discrepancy between bill and phone could be data used over wifi or slightly different cutoff time (phone could be running totals until midnight your local time and T-mo could be using pacific time).
If I had to make totally wild guess, I remember once somebody posted something about some program going wild on his phone and using gigabytes of data in a matter of days, don't remember the outcome, if it was virus or just crashed program in a loop accessing internet at random, but maybe you should start with some full reset or something. Also maybe look for a better program monitoring your data access and usage. I would be concerned and tried to figure it out, if it was my phone, especially that I have 2GB high speed limit, LOL. Is your phone set up as mobile hot spot? Could somebody else use data from your phone? Did you run virus check?