Paula,
Have you introduced new food to your LO? Once I offered prunes to AK for breakfast, and boy, we had one of those nights....she was crabby all day long and at night she had an awful diaper rash (I took about 1 month to clear away) and she vomited, vomited and vomited...
When AK was about 6 weeks, she had a very bad period with colic, and when I took her to the doctor, all she would do was smile, smile and smile. The Doc would tell me that there was nothing wrong with her and I swear, as soon as we were back in the car, the screaming would start all over again.
I took me about 10 visits to 3 different doctors and a gastroenterologist to get a simple medicine to reduce her colic; all the doctors told me that she was a perfectly healthy baby and that there was nothing wrong with her. If it was colic, she was going to grow out of it at some point.
My message to you: no matter what the doctor says, if you feel that your LO is not well, take him to as many doctors as many times as you need. Doctors might know their stuff, but you areThomas's mom and you know him the best.
I hope Thomas will get better soon.