Not sure if this is a problem or not, the game seems to work fine. I should note I have seen that deleting the META-INF folder results in Java saying it is corrupt if I try to load it from Windows Explorer.
Upon loading the mod into the JAR, my game no longer loads, but instead just runs in the background (but is recognized as an instance of Minecraft by the launcher). I seem to have issues with Risugami's ModLoader (timestamped 12-11-2010, I have two different versions a few hours apart, which suggests this isn't an incompatibility issue).
I like playing on alpha (1.2.6) and am trying to get the Battle Towers mod to work with it. So I am having a bit of an issue with Minecraft modding.