You may want to stick with one flavor for 2-4 bags (depending on how fast you go through a bag) and rotate every 2-4 bags instead. Switching to a new flavor, because they're all very different, is like switching to a new food each time so yes, that may be the cause of the stomach upset, especially if you're not taking the 7-10 days to switch over from each flavor. Personally I add about 1 1/4 cups of water to both of my dog's food and they do well with that. Each dog is different though obviously.
Tyson, white, 4 years, Boxer & Thor, 2 year old GSD
Tiger and Raven, kitties, 10 and 11 years
Erin flashy fawn, Lucas, Flashy Fawn, Boxer angels, RIP 11-29-10 and 8-22-07