Tried it with a Mekanism factory.
The manipulator extracts all items in the input slots, although the side of the factory where the manipulator extracts items is set to "dark blue" (=output).
This issue is still present in the source code, I just compiled a build from the master branch, the issue is still there.

Known bug and all attempt to fix it so far have resulted in no change. The manipulators work well with normal machines, chests, crates, etc however i think something is off with how Mekanism and assembly line work together. I'll take a closer look at it for 1.6.2 but there is no plan for a back port to 1.5.2 for a fix. For the moment you can use a hopper and a chest to get it to work correctly.

Fixed it and made a PR (#56)