Your bike is only running on one cylinder most of the time. Then occasionally, the other one will kick in. My 650 last week was doing the exact same thing. It started OK, but I immediately noticed that it was slow to rev up, even in neutral. And it popped every couple of seconds. I took it out for a run to see if I could ride thru the problem. Sure enough, after about 2 miles, the other cylinder kicked in and everything was normal.
I'm not sure what my initial problems actually was, but I suspect carb crud blocking a jet for a bit. You can touch your header pipes gingerly and tell if one side isn't firing. Careful, you can leave skin there too if you stay too long.