Are you sure that you are seeing a real reduction in runtime? After powering on, the initial reading might be a bit low because the hard drive is active. If this is the issue, the level will rise.
Higher bitrates (such as when playing FLAC or lossless wavpack instead of MP3) cause more hard drive activity, which can shorten battery life. However, what you play shouldn't affect what happens when the device is off. If you're really getting that much of a decrease in runtime while off, that's either a hardware fault or bug.