There were multiple reasons for this, most importantly the SSMEs were routinely used well past their rated thrust efficiency (you hear shuttle pilots being ordered to go to "104%" or higher on most launches) which essentially requires the engines to be completely overhauled and rebuilt after every flight.
Would you have any source for that? Shuttle main engines at 104% were not running beyond their spec. The final design of the SSME was capable of somewhat more thrust than originally specced, but for the sake of convenience "100%" throttle was calibrated to be the same amount of thrust as 100% of the original intended spec. IIRC the true maximum was 109%, which was indeed beyond normal safe limits and only used for emergencies.
We don't really understand it, so we'll give it to the programmers.