Radnen told me that one of the levels was unbeatable, because the secret is blocked off, and I noticed that if UpdateGame() wasn't commented, the game would go into a loop. I thought it was because of an error in the function, but after checking, I found out that the problem was actually because of laziness. The update function downloads a text file for scripts, maps, spritesets, etc, and in each line in each file, it looks like this:
http://eggbertx.theoks.net/secret_collect/scripts/main.js,md5hashofthefile
I had been uploading the files, but I forgot to update the md5 hash, and in my function, after it downloads the new scripts, it restarts the game to reload them, so long story short, the hashes weren't matching up.