The sync process is only one way and that is iTunes -> iPod. The only exception to this rule as you have discovered is iTunes purchases. If you want to copy/extract all other non iTunes purchased music from your device you'll need to the help of third party software. There is a method that doesn't require software but can be a bit tricky.
See this older post from another forum member Zevoneer for a few different options as well as more general information on copying content from your iPod back to your PC.