Aluminum liner is commonly used as this will not corrode, however, it should likely also be insulated as colder, slower moving flue gases will increase condensation and hinder the performance of your boiler. I would also like to highly recommend reading the product literature and paying close attention to the venting requirements for your boiler, as most natural vent systems should have a pressure switch that would shut down the burner flame in the event of downdraft or spillage to prevent carbon monoxide from entering your home. If there is no safety mechanism in place, there should be a draft hood installed at the flue collar. However, a more concerning cause would result in the issues you are describing. If your installer bypassed the pressure switch in order for the system to function properly, this would result in all of the problems you are experiencing.