If that's happening, it's a bug, but I'm unable to reproduce it. Can you post a screenshot so I know exactly how everything is set up?
Also, make sure you're running the latest version of the mod.
Yeah I have double checked and I have the latest versions of Engineer'sToolbox and EMasherResource installed.
Real simple setup that involved a chest and two sockets.
Socket #1 has an Extractor Input on top (for pulling out of the chest it is under), Item Output on the bottom, and a Redstone Input on the north face.
Socket #2 has an Redstone timer on the south face, placed on the north side of Socket #1 (so that the timer pulses to work the Extractor Input).
Connecting to the bottom of Socket #1 is BC's Golden Transport Pipe, heading straight down into a third socket that is configured as a Grinder machine.
Every time I see ore drop through the Golden Transport Pipe, it never gets subtracted from the stack of ore sitting in the chest at the top. If you still need screenshots, I'll come up with something.