TL;DR - if a mod sets temperature for a fluid to something non-default, recipes stop working (fluid doesn't enter the assemblers).
I have a heavily modded game but I think in this specific case only Factorissimo, Bob's stuff and bio industries matter.
My test case was as follows:
build a nitrogen generator inside a Factorissimo factory like this:
Nitrogen factory
It generates nitrogen from thin air with default temperature of +25C
I export it to outside factory that uses it in recipes:
Nitrogen usage
As can be seen, nitrogen in the pipes there does not enter the assemblers. Nitrogen in those pipes has a temperature of -196C. Only mod I could find that sets the temperature is Bio Industries.
What I think happens is that when the nitrogen is generated inside the factory it generates the Bob's version of it that has the default temperature of +25C. When it exits the factory it is "transformed" to be the Bio Industires version with the altered temperature. In the list of mods that alter nitrogen, Bio Industries is listed as first and last one to modify it with Bob's stuff inbetween.
When I tried feeding that -196C nitrogen to a recipe from Bio Industries that too didn't work the same way.
The reason why I think the bug could be from base game is that I don't think that temperature of fluids should matter if it gets used in recipes or not.
On the last screenshot you can see I have a few machines generating nitrogen inside the same factory that uses it. Those output nitrogen at the Bob's default of +25C and that version of nitrogen is used as it's supposed to be. The two "versions" of nitrogen can mix the same way as hot and cold water mixes (temperatures equalize).
If you need a savegeame and mod folder I can provide them on demand.
