These instructions are for MCUpdater 2.0. Quite a few things have changed since then, and updates are forthcoming. For more help, see us on IRC.
Please note. MCUpdater tries to muck with the Minecraft jar as little as possible. Old (pre 1.36) versions of MCU would constantly overwrite everything in the .minecraft folder, but newer versions store their data in a parallel .MCUpdater directory and launch your selected instance from there.
MCU will download the latest minecraft.jar for you (after providing your Minecraft credentials - your password will not be saved) and patch it to the necessary version. If you receive this error message, it is likely that you did not provide credentials or Mojang's download servers (on Amazon's network) are down.
Chances are the serverpack is messed up. The console log probably says what's going on. Usually a mod or config will have failed to download or the downloaded version may not match what the serverpack expects.
For more details and ideas on how to make life easier, see the Tips page.