I've recently had a similar problem making a game with javascript. I stated making it render with plain dom elements and transforms because it was simpler, however I noticed that sometimes it stuttered.

After looking at performance tab it turned out that dom modifications trigger uBlock to run it's internal checker(presumably to check in case you are adding some ads onto the page). It's not a problem in a normal circumstances, but when you are updating dom 10+ times a second it sometimes chugs. Rewrote rendering to use canvas and the problem went away.

Might me something similar here.