The Kye homepage has a screenshot of that level with three timer blocks in the bouncer area. I tried adding those to the level in the puzzlescript editor and it seemed to fix the issue above, though I'm now trying to puzzle out the rest of the solution, so perhaps I've only kicked the can down the road :)
edit: oops scrub that, I have now completed this monster of a level (phew) but it's the same issue as the first time round, where if you wait the bouncers will eventually just produce the solution without any player intervention. In this configuration, the collision between the vertical bouncer and the two horizontal ones seems to cause the lower horizontal one to desync from the upper one.