Ok, I set up a builder block as a quarry. I allowed all types on the shape card, no filtering. Turned it on and it started giving me cobble, as expected. I get a Storage Filter Module and set it up to blacklist Cobblestone and Stone. Insert it into builder and turn it on, and from that point on, nothing is quarried at all. For a bit, I thought it might just be a dry patch in the world, but after 2 chunks, I knew there was a problem. I took out the Storage Filter Module and checked the cobblestone and stone boxes on the Shape Card Quarry and turned it back on and the chest immediately filled up with lots of ores and other quarried items.

I'm sure I got the settings on the Filter Module correct, and even if I didn't, it should have either mined just cobblestone, or just other stuff, but ... nothing.

First: versions please

Second: Show me the gui of the builder and the filter card

Minecraft: 1.12
Pack: FTB Unstable 1.0.2
RFTools: 1.12-6.10beta4
Forge: 2407

GUIS: http://imgur.com/a/D4NSz

Try toggling the blacklist icon in the item filter

Toggling the blacklist did nothing to help

Not sure what I did, but it seems to be working with the filter now. Sorry for the issue, I honestly thought I had found a bug.