I think your doctor might be concerned about congenital dislocation of the hip - this is where the thigh and hip bones don't quite line up properly. It's something that can be fixed, so try not to panic! Here is a website with some more info: http://www.cyh.com.au/HealthTopics/HealthTopicDetails.aspx?p=114&np=304&id=1919
I read up on it as my MACH nurse thought my daughter might have the same problem because of uneven thigh creases (same as your bubby). We went to our GP and after he checked her over he said there was no problem. From what I have read, uneven thigh creases don't necessarily mean there is a problem, and your bubby probably screamed when your doctor checked his hips because it hurt, not because anything is wrong!
I am disgusted that your doctor did not tell you why s/he was referring your bubby for an ultrasound and xray - you are his mum and have a right to have things explained to you properly. Anyway, I am sure you are being referred just as a precaution - if there was a problem, it probably would have been picked up by now, so try not to worry (which I know is very hard)!
Hope this helps.