Well I'm certainly no vet, and my best advice would be to check with different exotic animal vets around you if the one you were using is unsure. It sounds like a possible infection to me, which apparently needs a good bit of testing and diagnostics to treat properly. MBD is a possibility, but it has lots of other symptoms including muscle spasms and swelling of the jaw that usually come with it. That doesn't mean MBD can be rules out, though. It would help if you could describe the diet you're using, or post pictures of the setup?

Here are some links from an animal hospital in long beach that talk about infection and bone disease that you may find helpful in the meantime;
http://www.lbah.com/word/iguana-infection/
http://www.lbah.com/word/iguana-bone-disease-nshp-mbd/