That said, I wasn't trying to bump/necro/troll anything, this looked like the most relevant thread, the comment at the top said the post wasn't confirmed by a dev yet so I posted here.
The game's machine alerting doesn't tell you if is it's halted by an unfinished pipe.
Unfinished electrical circuits will show up red, unfinished pipe was white and hidden by the lavatory. Just a case of fixitating on the wrong part of the map.
So... to the next person with a bio filter issue
Double/Tripple tripple check the path of all pipes from start to finish, make sure there are no missing connections
Ditto for wires.
P.S off topic - Is there a way that devs moderators can have a status flag by their name so we know whether we're chatting to a regular user or a mod/dev?