The rebuilders are really for your planets, rebuilding your own mines and turrets that get destroyed. They will only work on nearby remains if you don't put them in FRD mode.
The cleanup drones also work on mines and turrets that get destroyed, but they do so on enemy planets. In other words, they get rid of destroyed enemy turrets and mines, but only those that are nearby if they are not in FRD mode. If there are no destroyed enemy remains left, then there's nothing for them to do but wait until you kill more enemy turrets.
Most likely your issue is them not being in FRD mode, though I have not checked the savegame.
Hope that helps!