There have been instances of people having myotonia with only one recessive mutation found during sequences and there are a few reasons that might be, such as the mutation not really being recessive, or copy number variation. There could also have been a lab error.
When genetic testing fails to turn up CLCN1 mutations or SCN4A mutations, in the presence of electrical or clinical "myotonia", and your doctor's have no other ideas, it's probably time to contact one of the ion channel specialists who deal with the more exotic forms of myotonia, like Dr. Tawil or Dr. Ptáček.