As of a few days ago, all non-belt connections to factories stopped working. I no longer even see the directional arrow to indicate input/output/balanced modes. Belts will still perform as expected, but chests, pipes, and bulk pipes do not.

EDIT: I'm an idiot. I was playing in sandbox with god mode, but didn't have containers and pipes researched yet. Since a post like this would have helped me realize my mental limitations earlier, I'll leave it up in the hopes that someone else can benefit from my mistakes.