I tried to extract items form the digital miner the way I'm acostumed, but the items were still in. I tried Itemducts, Ender Conduits and the Logistical Transporter. Did I configured something wrong?

Forge: 2755
Mekanism: 1.12.2-9.4.13.349.jar

The other ports did not work. And it only works with Mekanism's logistical transporters.

Found out, that the port on the back has to be used.

Any of the gold/yellow ports should work afaik

You can just stick chest to the back output. The uper one is used for materials to fill out the holes. At least that's how it worked every time for me :)