No, the fan is on, but when I used "--auto-fan" it showed up as 0%. It was actually running the entire time. I don't think this is a bug with cgminer (I haven't seen other people posting the same question), but rather it's probably due to Xubuntu. There are a handful of posts about GPUs not running their full hash rate IF they are on Xubutnu AND have multiple cards on the MB. I also had problems with this, and for me, the workaround was to start cgminer with a monitor plugged in. I can unplug the monitor after starting, but it has to be there at first. Other than that, it works great.