when you installed Mac OS X, did you apply any updates from disk that were not downloaded through Software Update? Installing from 10.1 and getting to 10.1.3 is not tricky per se, but you do have to let the SU app download and install the updates in the correct order. There is an update to the actual SU app that is required for it to get future updates. If you did not install that, then that is why you SU is broken. Check your /Library/Receipts folder or check the SU history to see if you did indeed update your Software Update software.
How convoluted was THAT sentence "Update your Software Update software"