If you didn't have sequencing on SCN4A, then you're probably right about it most likely being hyperkalemic periodic paralysis or paramyotonia congenita. Although new mutations are being discovered all the time, it can take 6 months to a year for them to show up on the international databases.
I would encourage you to send a sample to Dr. Lehmann-Horn's lab along with the report so that they know which exons were already checked.
The testing for myotonia congenita (CLCN1) is almost 100% accurate now. But the sodium channel testing is still improving and I believe the last estimate I saw was about 60% accurate.
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.