I don't know if this is the same problem I had, but it sounds similar to a problem I had with the stock sprocket (44) and the 36 I bought.
Obviously, in an ideal setup, the chain would run perfectly straight from the motor to the rear sprocket. This is not always an easy task due to the near infinite amount of differences in engine kits, sprockets, bike frames and whatever other variables that could make a perfectly straight chain path difficult (or impossible).
After my kit was installed, but before I rode my bike anywhere, I lifted the back wheel and started pedaling the cranks with my hand. (while the bike was leaning on my kickstand) Immediately I noticed that every few seconds or so, the chain would make a loud snapping sound. The sound was coming from the chain not grabbing the sprocket teeth on center (so it would not seat properly on the teeth) and when the tension got high enough as the link would go around the sprocket, the rest of the chain behind the link would violently snap back on the sprocket. There was NO way I was going to fire it up with the chain acting like that. I didn't even pedal ride it anywhere.
However, after a quick investigation I realized that it was happening because the sprocket teeth are hard edged and very squared off. What I did was, I took a dremel tool and made ALL the teeth pointed (Instead of square edged) so that it would be impossible for the chain to grab the edge of the tooth and as a result the chain has a FAR easier task of sliding properly onto the sprocket teeth. After doing that, it COMPLETELY solved the problem with the chain. In fact it may have even reduced the amount of friction the chain experiences as it goes around the sprocket.
Something to try...
BARRY