Okay, more data. I'm playing on a Mac.
Playing version 0.9.12 "Spleen", the very first enemy I kill in the game is worth like 200 points, and the multiplier goes up by 0.2, then 0.2, then 0.4, then 0.4, then 0.6... I finish level 1 with about 3000 points.
Playing version 0.9.14 "Brains", the first enemy is about 100 points and the multiplier only goes up by 0.1 each time no matter what. I finish Level 1 with about 1000 points.
I seem to have missed 0.9.13, so the change could have been there too.