My wife's T800 (2007) has been a good bike. I did have to replace the Bottom bracket after about 6000 miles. It was a Shimano. Your's is a Truvativ, but they are both splined. The frame has very little or no relationship to how the components perform. Have the LBS remove the crank arms and spin the BB spindle by hand. You will feel it if there is a problem. Also check the torque on the bottom bracket, crank arm bolts,and chain rings.
Cable tension on the rear derailleur is also sensitive on her bike. If not adjusted correctly it will "skip" gears.
I have never encountered it before, but my wife's BB drive side cup backed out a couple of turns on a bike I built up for her 2 years ago. It was also making a rotational related noise. I am usually pretty careful about torque when putting a bike together, but I must have missed it on her new bike. I'm not sure why it decided to do that after 5000 miles, or how long it had been that way.
I have a LHT, and can tell you that if it was stock it is no better than the T800. For the most part, the T800 had better components than the stock LHT does.