Really weird issue going on, no clue if it has anything to do with the mods I'm using. I don't think I have anything that impacts how fluids work, just stuff that adds non-vanilla fluids and storages.
Using "James Oily Extravaganza," I have a fractionator splitting crude oil into five different fluids. Except three out of the five output fluids just seem to vanish. They don't accumulate in storage, they don't pile up in the pipes. They appear momentarily in the pipe/tank system, and then disappear completely. The three that vanish are produced in far smaller quantities than the two that actually persist, but I'd expect them to simply accumulate at a lower rate than the other two.