I just went out and re-checked one of my eccentric hubs, and the bolt does go all the way in on it. There is a separate collar under the bolt head with a small flange that is meant to fit in the drop-out, but that flange is small. Maybe 1/16". No dropout is thinner than that.
I suspect that there is a rough spot on the threads you are feeling. Maybe clean the threads up as much as possible and put some grease on there, and then maybe work the bolt back and forth to see if you can't get it to go in further. Having said that, I am merely an owner of some of these hubs, I cannot say with complete authority that yours is the same; so be careful. Its a beautiful hub, and worth thinking before acting.
jim
p.s., D'uh. My earlier question about it being a QR on an eccentric hub was pretty dumb. Sorry.
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