Julian,
How stars appear in your sky flats depends on whether the mount"s tracking is on or off, not on guiding. With tracking on the stars will be bright points and with it off, there will be dimmer a star trails. I keep tracking on and dither. I'm using CCDAutopilot which automates sky flat acquisition. With tracking on, CCDAutopilot dithers 6 arc minutes between flats. This insures the stars will not be superimposed and are easily rejected when the flats are integrated. For light frame acquisition, I dither 2.5 pixels.
HTH,
Steve