Definitely check and watch the trap. After that, you may go through a few before things settle down. It may be worth getting one of the big "can" traps to scrub as much as possible and then use a smaller indicating trap to check.
Unfortunately too, helium can be hit or miss these days. Water can be pesky, and if there was a bunch of it it's possible it's still popping out of your fittings or is taking its time to work out of the nooks and crannies of the MS(the ceramic insulators can be like a sponge).
How's your high vac? If it's abnormally high for this system, it's worth doing an extended(~8h+) bakeout of the source and quads, and of course monitor the hi-vac over that time. My Varian triple quad had a nice feature for the bakeout cycle where it would plot the hi-vac vs. temperature and time so you could see if you were doing anything. I've not seen that on HP/Agilents, the only other MS I have any great amount of experience with.
As for the filament life-first of all, are you doing CI? That can really beat up the filament. When I've done CI in the past, I would cycle the filament on and off once I'd established a method and knew the RT of my analytes. There again, going back to the Varian TQ, which is the only place I've done CI, the $300 filaments(single too, not two on one insulator) made me very protective of them. A high background of anything is rough on filament life, and your high water could be the problem too.