I'm not quite sure what to do but I did ask a few other people about the cracking (maybe flaking wasn't a good discription) and most thought that I may have used too much water when mixing the grout. Someone even suggested that during the curing process I should spray the grout lightly, keeping it moist as it drys. Make any sense to you?
I'm inclined to dig out the cracked sections of the grout and regrout those areas using less water. The only other option seems to be to remove all the old grout and start over. Ugh!