If you have under 50K miles, perhaps 100K- you would have to check into it-, it might be under an EPA emission control warranty. You know, leaking a hazardous material onto the road bed when the vehicle is under a warranty.
Or, the 100K mile engine warranty. I never used it, so I am not sure, but aren't our engines under a 100K warranty that includes everything? Including leaks? I would think that a leak would be evidence, or in medical terms- a symptom-, of a larger issue. An issue covered under the 100K warranty.
I remember a few years ago I never had a problem with warranty work. But in the last year or two, with the auto companies dying as they have been, it has been tough getting them to stand behind the warranties.
Does not the Magnuson/Moss act make it ok to use after market filters and such? If the filter company specifies your engine is it not ok to use it without voiding the warranty?
You may want to contact a company such as this one and ask them.....
2003-2008 Ford Truck Problems - Diesel Engine Problems
Though your warranty booklet may be your best resource. It may have everything outlined as to what is covered.
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'03 Excursion, 7.3L, 4X4, Auto tranny of course (they all did), 4" MBRP exhaust, TS performance chip, K&N FIPK w/ an Amsoil EA filter, Hellwig anti-sway bar, drilled/slotted front & rear rotors. Rancho XL shocks, Rancho steering damper, Airlift 5000, S&S Diversified headlight mod. This baby surprises a lot of, so called, performance cars. 
'04 F 350, extended cab, 6.0L, FX4, manual tranny, 4" MBRP exhaust, Bully Dog Triple Dog downloader w/ Outlook moniter (Very disappointed in the Bully Dog), 2m-70cm Yaesu ft-8500, S&S Diversified headlight mod.
'96 Mustang Cobra convertible, B&M short throw shifter, Koni adjustable shocks, viper chip, drilled/slotted rotors front and rear, rear sequential turn signals.
'11 Harley-Davidson Road King Classic 103 ci PowerPak w/ anti lock brakes & Smart Security system. It even has cruise control!!! Candy Dark Root Beer over Candy Light Root Beer  Yaesu FTM-10R & a Comet CSB 790A
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