this would mean it isnt firing at top dead if it is off 180. the cdi could be telling it to fire to late or to early. as long as you have spark and it doesnt clank when you are trying to start (firing to early) I would back the chain. sounds like it might be trying to fire when piston is already going down. If it was firing on the way up the noise would be noticed when it fired. You are getting a nice blue spark right? I would also check all fuses in it when my 125 got a little warm and back fired it blue a fuse and would not start. Might be the same when it jumped time and fired at the wrong time.
Just my 2 cents
1982 Honda 185 My work horse
1985 Honda 125 kids love it
1984 Honda 200S My main ride