This most likely explains your situation (please listen):
Evidence of denervation in an EMG (PSW's and fibs) takes time (up to weeks) to show-up. Therefore, the reason your intial EMG's were probably clean is that the denervating process that occurred (I know that it occurred because you now have evidence of reinnervation) had not occurred yet or the EMG was done too early to catch it or the EMG was done too late to catch it. Why too late? As soon as a muscle reinnervates, the evidence of denervation (again, PSW's and fibs) disappears, unless the process of denervation is progressive (your's obviously isn't, which points away from ALS, if you were wondering).
Evidence of reinnervation in an EMG (large MUP's) takes months to show-up. Therefore, what caused your denervation only caused it for a short period of time and your initial EMG's (as I stated above) simply missed it. Your latest EMG was done long enough after the denervating process to finally show the evidence of reinnervation.
If you are still asking why you don't have ALS (I know you are): With ALS, the denervating process is ongoing, so someone with ALS will have PSW's, fibs and large MUP's in their EMG . . . and . . . it will be in multiple areas of the body. Furthermore, even if someone has these findings, it wouldn't necessarily mean they have ALS; it would have to be correlated clinically and it would have to be progressive.
Your EMG is not even close to the EMG of someone with ALS . . . your clincal exam isn't even close to someone with ALS . . . your progression (or lack thereof) is not that of someone with ALS. Ergo, the reason your neuro was absolutely sure you do not have ALS is because THERE IS ABSOLUTELY NO EVIDENCE YOU HAVE IT . . . NONE . . . NADA . . . NIHIL.
Now be done with this.
P.S. If someone comes back with . . . "my clean EMG might have been done too early to detect ALS" . . . I'm going to shoot you. Read what I wrote again if you have that question in your mind. Furthermore, with ALS, the denervating and reinnervating processes have been ongoing for a long time . . . much longer than anyone would realize via clinical symptoms. Therefore, the EMG of someone with ALS would have PSW's, fibs and large MUP's from the very beginning.