I have a 14 yr old Peerless Boiler with two zones. The downstairs is very responsive, but upstairs is inconsistent. If it get chilly up there, we turn it on and everything warms up. The thermostat snaps on and off accordingly. The strange thing is, when the thermostat snaps off, of when I turn it off, or even when I turn it off at the boiler, the pipes upstairs stay hot for another 3+ days. Any ideas?

When you are turning it off at the boiler, do you mean a switch or a valve? If it is a switch, the zone valve could be leaking allowing hot water to continue to circulate. It could also not be closed, when it signals it is closed. If you are manually closing a different valve, perhaps I could figure it out if you give me more details on the system.