Recently I was in my attic & noticed water damage located right below a vent stack. I checked the exterior boot & noticed the bottom portion of the boot flashing was nailed down. Is this proper installation to nail the bootom portion of the rubber boot flashing?

Should it only be caulked??

Thanks for any input
MDB

I have a Comfort II program with four zones and a Payne High Energy Efficient heater. The heater comes on for only several minutes and then shuts off. There is a continuous running of the vent. Any suggestions?