Boiling water in the overflow bottle can be caused by a ruptured head gasket, allowing exhaust gases into the cooling system. But, you are not experiencing over-heating, which would be the case if the gasket was ruptured.
As my C5 Corvette friend suggested, check to see if a siphon is occurring during cool-down. The coolant in the over-flow bottle should be above the fill mark when hot, and lower when cold. If the coolant isn't flowing back to the radiator, there is a breach in the closed system allowing air into the system.
Without a siphon, you will keep losing coolant, and eventually over-heat.
If air is entering the coolant, you can pressurize the system to locate a leak using a loaner tool from most auto stores that fits over the cap neck of the radiator.
Also, check the gasket on the rad cap for deformity. A common problem.