2007 2500 running rough with update 9r06

[southerncomfort4x4]

I have a 2007 2500 5.9 CTD and usually run my U7131 on performance, normaly it runs great but it was recently updated and now runs noticably rougher especialy at idle. Last week i was 4 hrs from home and had a code P2146 & P0203 and had to replace #3 injector!!!
Was there more injection timing added and could the tuner have been the cause of the failure? Kind of has me afraid to run my tuner. I also dont have any injector knock with it on my stock program and it idles sooo much smoother.
PLEASE Help!

Thanks in advance for the advice!
Michael

[mikel]

Injection timing is where the mileage gains come from, sounds like a rather common injector failure.