I have learned after going rounds with several doctors regarding my son's health, that Doctors often require high-level communication skills when trying to convey concerns and get information. Did you ever find yourself in a math class completely lost because the teacher seemed to be talking over and around your head and not directing your specific questions? We want our doctors super-educated, but sometimes the communication is the casualty. Personally, I'd rather work on my own communication skills than settle for a better communicator with less medical knowledge.
We have to take more responsibility in the process. While there are some doctors out there who just don't care (especially about parental input), there are options. If you honestly feel like your child's provider is not providing the best in care because they don't listen to the primary care giver, change providers. Keep in mind, though, sometimes your concerns are related to such simple or mundane and normal processes of the body it doesn't seem like much of a talking point to them. Always be ready and willing to assert yourself. It's for your kid. No one will blame you.
There are a lot of details necessary to discern exactly what might be causing your son's popping joints. If he is very young, it could just be that his body is still developing. Young children have a lot more cartilidge. It's one of the reasons they are generally more nimble and ressiliant than adults. If you are concerned, though: Don't let it go. Next doctor's visit, go in prepared with a detailed outline of the rate of occurance, dietary intake, and any corrolations you may have noticed.
Best wishes to you and your dealings with the medical profession.