Shaun,
Please note that the USP standard with the largest amount of chlorine gave you the problems. If a FID burns an analyte of chlorinated composition, a by-product is HCL. If there is enough silicone residue on the ceramic components enough HCl can be depositied on the 'insulators' to where they do not insulate well. I have seen strange behavior on such contaminated FIDs.
This silicone residue is usually from phase bleed or decomposed silylating reagent used in preparing samples. But since this instrument was used for headspace I suspect it is from phase breakdown of the G43 phase on the thick film column used for USP <467>. Water, oxygen (air), and temperature on a silicone phase is a receipe for phase breakdown, and have I not described a headspace injection?
I hope there was some visual indication of the detector insulator contamination. If not, then remember to schedule cleaning on a regular basis, whether you need it or not. I always prefer to keep spare parts, clean and ready, to trouble shoot inexplicable problems as you described.
I am glad you found the problem and pleased that you took the time to tell the Forum the end of the story. Thanks !
best wishes,
Rod