How can I ensure that the clear plug valves are seated properly?
Prior to inserting the plug into the valve base, moisten the surface of the plug then quickly insert it into the base. Doing so will allow the plug to slide more freely into the base until it bottoms out. The moisture around the plug also helps seal it (kind of like getting a suction cup wet before you stick it to glass). These valves not being seated fully down into their base is a common reason for air leakage in smaller air chambers of your tube.