The pilot on my propane boiler won't stay lit for more than 30 minutes even after replacing the thermocouple and outside gas valves. The inside gas valve was replaced two years ago. Service people are stumped and it is cold! It is a Crown Boiler.
If the thermocouple is new, and we assume that it's good, then I'd wonder if it's positioned correctly? I don't know how your boiler is, with some of them you can re-position the TC with respect to the pilot, and it might be too far away.
On a similar vein, are you sure it's locked in place and can't move? For instance, if it could vibrate around a bit, it might be moving too far away and therefore getting confused and cutting the gas.