A monitor connected to the HDMI socket on your D6000 will not be detectable by the DisplayLink Manager software because the assumption is that HDMI acts as DP alt-mode when both DisplayPort sockets are occupied.
What I propose next:
- I would check that your D6000 has the latest firmware. Dell have released a tool to update this, but it's only available on Windows, so you'll have to connect it on another computer for the update. You can download the firmware here.
- Disconnect the monitors connected to the DisplayPorts and check that the monitor connected to the HDMI port works. It should work both with DisplayLink Manager on and off.