Thanks for your feedback, it's really appreciated. Your first instinct was right, the color of the orbs does deliver more damage if you match up the enemy's color. Unfortunately we still have a little bit of work to do on balancing, because whether you deliver 1 or 2 points of damage to an enemy with 1 hit point, they're still equally dead. =) But it does matter a bit more to the longer "replicators". If you hit them with the wrong color they multiply.
Your feedback on the glitchy interface is good stuff, too. Thank you!