Hi Froggygoloso,
If you're still struggling with this, this might be worth a try - apologies if you've already tried something like this!
When I'm making games with PixelBox I usually move the actual update logic outside of the "exports.update = function so the main.js ends up looking a bit like this:
It's probably not strictly speaking the best way of doing this, but you should be able to make sure that your recolouring code runs before you start drawing things to the canvas. It does depend a bit on how exactly you're trying to do this at the moment, but this should let you effectively delay things.
Hope this helps - if not I might be able to offer some more suggestions if you're comfortable with sharing some code here, but no worries if not!