Tested by setting the boost rate at 10 catches and above to 2048x in the config, spawning and catching ~15 Arons, and then waiting for natural Aron spawns. None were shiny, when you would expect at least one or two from such a high rate.

Thanks for the report! I've tested this, and it seems Catch Combos (or maybe just the config, not exactly sure) are broken on the latest version. I've gone ahead and forwarded this to our internal tracker. Have a nice day!