Micro instances only provide "burst" CPU usage - if you keep above a certain threshold for long enough, it will throttle you by stealing CPU time (hence the 99%).
Would be nice if they could/would average out the cpu usage over a longer rolling window. That'd be perfect for a use case like this (build server) where you're idle the majority of the time but want to max out cpu during the build itself. Seems like the perfect use case for a shared server.