When you are pixel peeping it often looks worse than you might like, but you have to look at the desired size you are shooting for. At least try it at the higher ISO rates and don't check it on the camera itself but on a (good) monitor.

I wouldn't negate the possibility that some manufacturing defect could be present on both the lenses. If they came from the same batch (which you can check with the serial number range) it could even be more likely. You could try to ask your store - or even better: a different one - to try it with a another lens (same type of course). And see what happens. As none of your other lenses have this problem, and the problem exists on different bodies I would still suspect something is wrong with that lens... and don't use the filter (I just noticed). And check the filter as well on another lenses.