I forgot about the other test...I guess we'll see...but this is maybe the biggest mystery I've seen in my time on the site, lol. The booklet doesn't say to shake it? Huh. With the nitrAte test it's super important to shake...but I coulda sworn all bottles and tubes needed it to some degree. I agree it's probably not the sole cause, but worth trying.
And yeah, that PFS is awesome. Once you switch to it, it's all you'll ever put in your tank. it does cause me to vacuum a few times a week since any waste sits visibly on the surface (I'm aquarium OCD), but there's no such thing as too many water changes and it's great to not have all those organics gathering under a gravel bottom and fowling the water.