When there are many chains of the same length, then it picks the one formed most recently. If there are still multiple options, then it's basically random. I did consider doing highest scoring, but then you lose the option to try and control it a little to control the area cleared.
It might be something I look at after the jam, though I'm already planning on creating an option allowing you to move the tiles in a round then lock in (you weren't the first person to request this!), and I think this makes the chain forming logic a bit more obvious, or at least I hope so.