Jason, I have bought a bunch of router bits from MLCS and have always been very happy with them. Did you contact them to advise of a problem? Can you check dimensions to .001" or preferably .0005" pretty accurately and on centers if possible. Not that you should have to, but it might help to define the problem for them.
For what it's worth, I ordered a bit that came obviously bashed up pretty good. The bearing was a wipe-out but that was all I saw that showed damage and that was hidden until you tried to turn it.
I called and they said that they had a rash of that in one size and shipment, because of that, they were out of that bearing. I had a good bearing on another bit so I told them that I would just switch, no big deal. They sent a bearing that was rough but still a lot better immediately and they sent a perfect bearing some time later. No charge for either, which is pretty good for a $12 router bit.
Actually, one of the woodworking magazines rated router bits a while ago and MLCS was ranked pretty highly, beating some bigger names that had prices twice as high.
Based on my experience, I would give them a chance to fix the problem. If you have, then do what you have to do. And totally from my experience, I would give them another try, perhaps on less complex ones until you get confidence it what they can do, or lose it totally. I'm sitting near a picture frame, bookshelf and table all made with their bits