2003 Ford Explorer All wheel drive

I have a 2003 ford explorer with all wheel drive. I had a flat tire, so I put on the spare which was brand new and drove home. I went and had a new tire put on the other side and the old one one the spare. So I had two new tires on the back. Not long after I started to have a thumping noise in the front in, it felt and sounded like I had another flat. Took it to the dealer, they said it was the tires so we had two new ones put on the front, so now we have four brand new tires. We leave the dealer and it was still happening. We took it back and they said we needed to replace the transfer case, so we did. It was still under warrenty. A few months go by and it is happening again. Took it back to the dealer, now out of warrenty, they said it was the transfer case again because all of the tire were not exactly equal in circumference. He also said if we have another flat that we have to have it towed and get four new tires, or be buying another transfer case at a tune of 2000.00. I have never heard of this before, was just wondering if you have and what your take on it is. If the tire differential was so important why did they not tell me when I bought it. We were told by the service guy that the allowable differential in each tire had to be less than 1/4 of an inch. Are all tires perfectly round and all the exact same size? HELP!