Hi. What you are describing is actually normal to have happen. I know, sure as heck doesn't make you feel better to know that. I'm sorry you are going through this stupid doubt from doctors. I actually think it's more about them and their frustration in not having a magic bullet test than it is about your signs, symptoms and test results pointing to MG, then not.
The fact is that SFEMG's are NOT positive in all people with MG. If you read a lot of the reputable studies, it's clear that they aren't. No test for MG is 100%. And there are even some MGers, like me (so far) who only test postitive for the modulating antibodies.
There are other drugs, like Advair, which interfere with EMG's and antibody tests. Even a small amount of steroids can make it look like you're fine.
I laugh when I hear or read neurologists say that MG is the most well-understood autoimmune disease. If it was, it wouldn't take doctors YEARS to diagnose us now would it?
The SFEMG can be negative if done in a muscle that isn't clinically weak and if it's early on in the disease process. It can also be negative if the person doing it is not REALLY good at it. And like I said above, it can be negative if you are on certain drugs like immunosuppressants (their "job" is to make the signs of MG disappear!).
Antibodies don't occur for no reason. Period. I know neuros see the SFEMG as the gold standard but they might want to start thinking in other terms since so many MG patients are not getting a firm diagnosis because of that. And then they are not getting the treatment they need right away either.
Mestinon too can affect the SFEMG, if you're going to have one again. There's even a study that states that Mestinon suppresses the humoral immune system and, therefore, can affect antibody production. So Mestinon may wear off within umpteen hours but it's effects may stay in the system much longer.
After all I've been through, I guess I would suggest doing something fun. Stress is not good for MG, and you obviously have it. It'll also help you take a new, fresh approach with your doctors if you are not full of stress. You might actually have to act like the "parent" and state the obvious like "then why do I have MG antibodies?" and watch them backtrack on their stance that you don't have MG.
One note about lupus tests. I volunteered to our local chapter for 10 years so I know a lot about it. When you have an autoimmune disease like lupus, you never get rid of it. Even celiac disease is still there and can't be "cured" but at least you can get rid of the symptoms permanently with that one. Lupus symptoms will come and go. You can flare with stress, heat, etc. just like with MG. So the test results can "flare" too!!! You can have normal lupus tests one month and literally have them off the charts the next. That's why it's good to have them tested when you are in a flare.
I hope you can get definitive answers soon. Like Scots Kat said, it is the worst position to be in.
Annie