[Rick Parker]

Are you speaking of the stud that secures the air filter assembly? That is pretty unusual to have that happen. Try using some Thread locker/ Locktite on the stud and the jamb nut and use a nylock nut on the top. There does not need to be a lot of clamping effort, just enough to pull the lid down to create a seal. The stud is long enough that it may not be able to navigate the curves in the manifold if it is in there......weird. If it got to a valve you certainly would have heard bad noise.
One thing I used to do was have a nut on the stud that would limit how far the lid could be pulled down. The lid essentially was sandwiched between the two nuts, the one under it was a flange nut secured (after trial and error fitting) with Red 262 Locktite.