I've check this before, i never had problem with them or theirs cockpit, i've made my test with two ships :
I firstly load each one in a different mission where they were pre-selected in the mission by fred, then i just load the mission, don't touch anything but pressing the launch mission button,
the cockpit where there as usual.
After that i reload those mission and select the "other" ship in the two mission, after pressing the launch button, the cockpit weren't there.
I've then tryed with all the ships where i set a cockpit model pof and it behave exactly the same.
In fact it remind me a "bug" i've met sometime ago where, when you use "change ship class" sexp on the player's ship, the cockpit may disapear. i guessed it was because that the sexp was designed to be used on ai.
I don't know if it may be related.