To answer my own question for anyone else, DisplayLink still doesn't support colour calibration so F.lux cant be used on a second monitor that is connected with a DisplayLink. Only monitors directly connected.
From F.lux - "I have a DisplayLink USB monitor adapter. Is there a way to make f.lux work for this display?
DisplayLink has no support for color calibration, so f.lux can't make changes to DisplayLink monitors. Unfortunately, you can only use f.lux today on displays that are directly connected to your computer. (e.g., it usually won't work over remote desktop either.)"
From F.lux - "I have a DisplayLink USB monitor adapter. Is there a way to make f.lux work for this display? DisplayLink has no support for color calibration, so f.lux can't make changes to DisplayLink monitors. Unfortunately, you can only use f.lux today on displays that are directly connected to your computer. (e.g., it usually won't work over remote desktop either.)"
http://justgetflux.com/faq.html