I had trouble with this boss too - I was trying to be "clever" and was switching between Nature, Beast and Energy forms... and at one point, the worm seemed to get kinda stuck on one of the walls :X That's actually how I killed it, I think. I don't know if that's a bug or if it just wanted to hang around.
My comp crashed a while ago, and while I finally got Aquaria working, it's had a few mini bugs that let me know something is still wrong... and I wondered if that was what this was. Sometimes places on the map flash and they're not supposed to be there at all on that area's map, and sometimes the darkness effect/light effect is messed up. Sometimes I could see what I wasn't supposed to, and the Sun Form's charged ability didn't always work right away. Not bad enough that I can't play, it's just a delayed action.