i am a maintenance tech for a large company and we install machines and hoists(not car lifts but tall hoists very similar) and we always drill all the way through the concrete(like matt said) so that when the "boss's" want to move a machine we just punch the anchor down and slide it where it needs to go. we get one or two that anchors that usually never fully tighten up, in our situation this is not a major thing as everything is stable. in a lift it would be a different story, if you have the capability of drilling out the hole and going to a bigger anchor that would be the best way i can see of fixing the tightening issue.
the main cause i have found of them not "biting" correctly is due to a "wobble" while drilling out the hole, usually just a warn out drill bit or someone not quite paying attention.
i would say just keep an eye on those bolts see if they loosen up at times, if they do you may try taking some form of 2 part epoxy and mixing it all up and stuffing it down the hole, mix some on the bottom part of the threads and swedge, then pound it in and let it set up before you torque it down.