Minecraft Beta Won't Launch

Hello, I am new the modding scene and I have been working with MCP and modloader on beta 1.4_01. All changes I made worked smoothly in MCP. The game ran and the mods worked. When I dragged the reobfuscated files into the minecraft jar and ran minecraft from the launcher, it would either black screen, crash, or get stuck on an "updating minecraft" screen. To test if any mods worked, I installed one really quick (modloader was already installed). It ran perfectly. I then created a blank class, compiled it, and threw it in there. It didn't start. I tried launching minecraft from the command line and that worked, I'm confused as to why the launcher doesnt like only the files that I create.