My hunch is it has less to do with whether they are made by Cosina or any kind of optical/mechanical issues whether real or imagined. I would guess there is a very small market for used ZE lenses compared to Canon L lenses. This means that since ebay auctions only run for a given time you will get less bidders on your ZE lens than a comparable auction for a Canon lens would get (relative to the number of lenses for sale). In any second price auction, the expected sales price increases in the number of bidders. Hence, the Canon lenses are selling for more.
So far the theory. The empirical evidence kind of supports this. Many items that are only sold in small numbers, seem to be sold through the fixed price mechanism on ebay. Maybe it is because of the lower fees, but I would guess it is because of this phenomenon. This has nothing to do with the quality of the itmes (I was looking at Leica R lenses, for example). So, unless you are pressed for time, putting your lenses up at a higher price waiting for a high-value buyer to show might make more sense.
All IMHO, of course.