Regarding trust and the stats.. I think the best way for you to know is to test the stats yourself.
This type of email kills me – we are already on the defensive. And solving this issue is sooooo tough. We do pride ourselves on our clean tracking.
I’ve had affs in the past come at me with the same email so many times, and my response is – Why do you think the stats are way off? Lets test the stats together.
Regarding conversions, what works for one aff may not work for another, which is why you see some threads where one aff says they are doing great with a program, and another aff will post they are not doing so great with the same program. The best way to find out which brands are best for you is to test and rotate the brands on your site. Find out which one converts best in each position and go with that. Other affiliates can suggest their top earners until the cows come home, but what works for them may not work for you and vice versa..
So, conclusion… TEST TEST TEST!