You have to learn how to utilize the boxes. If you're going to fast, you want to hit the box instead of jumping, because it will slow you down and you have more control. You want to be fast enough to make the jump, but slow enough that you can still see when you're suppose to jump. Nice game.
The glitch that happens after three rooms can be fixed. You just go into your book, and you'll see that the Hawaiian song is unlocked, even though it didn't make the noise. I hope this helps someone, I know it did me :)
The end says "Thank you, organism" which leads me to think that I was just put through a situation similar to how animals feel when being tested on. They do what they are told, and get a reward (in this case a banana). Nicely done :)