there are other blogs about it, so i won't reiterate the problem itself, but here is a theory to reconcile it:
if you go with the theory that the wheel chamber was dislodged from time like sawyer and crew were when the wheel was rocking back and forth, and that is why locke was able to fix the problem despite being there in a time before ben would have turned the wheel to create the problem in the first place. then this may be possible:
the area dislodged from time is proportional to the problem in the mechanisms of the wheel, and this area may be big enough to encompass the entire island.
the plot line would go thus: the smoke monster assumes the brothers form and rebuilds his wheel project. while testing stuff out, he uses too much water with the light, or something, and creates the same problem ben did, but to a much larger degree, so the time bubble encompasses the entire island and not just the wheel chamber.
the island moves through space to a new location, but begins bouncing through time in that new location. smokebrother fixes the problem, but the time bubble leaves the island in a suitable egyptian era, or even earlier. the egyptians are brought by jacob, or find the island, they explore and build, become the first others, etc.. leading up to the black rock, dharma, the plane crash, etc...
keep in mind this would mean that for a length of time there are two islands, but occupying different spaces, like the end of back to the future when marty sees himself in the mall parking lot right before going back in time.
there is the problem that when sawyer and crew were bouncing through time they were always on the island, despite the island having moved its position in space over time. so for this theory to work you have to assume that the shifting through space as well as time for sawyer and crew and wheel room was a result of something in the wheel room mechanisms, and not the inherent nature of the island.
as for smokebrother not being able to turn the wheel himself, we'll say jacob made up that rule after smokebrother threw them back in time.
so there you go, i can't think of anything this contradicts in the show, other than making jack even more off base about the adam and eve thing. so add to it, or find problems with it and let me know.