EMB170 Captain reports starting down late for a crossing restriction at BOONE on the ROYKO3 arrival to ORD. LOOTH is after BOONE and has an expect altitude of 11000 FT which had been entered into the FMC. The reporter assumed the FMC was set to make the assigned crossing restriction.

Narrative

We were filed for the ROYKO3 arrival into ORD. We were cleared direct BOONE (fix on the arrival). A few minutes later we were instructed to cross BOONE at 11000 FT. I set the altitude in altitude select box; confirmed with First Officer. Set the autopilot for VNAV descent. As we approached BOONE; I realized the airplane was not going to cross BOONE at 11000 FT; so I overrode the FMS and told Chicago Center we started the descent a bit late but still we were going to try to make BOONE at 11000 FT. After a quick calculation; we realized we were going to make the crossing restriction at BOONE; but ATC instructed us to cross LOOTH at 11000 FT. We made that crossing restriction. On the arrival chart it calls to expect LOOTH at 11000 FT and that was what I had in the FMS. That was the reason why the airplane was not going to make BOONE at 11000 FT. I think there is too much similarity in the two fixes (LOOTH and BOONE) and that can create some confusion. No further incidents were encountered during the flight.I should always make sure the altitude restrictions in the FMS are the same as the one given in an ATC clearance and also expect any type of change in those restrictions. I would also like to see a change in the ROYKO3 arrival. There should not be two similar fixes where one has an expected crossing restriction (LOOTH) but when in reality ATC assigns the crossing restriction to the other intersection (BOONE).