I posted the question on another group and Stan Moore the author of CCDstack answered. Here is his answer about whether to subtract a bias from your flats when making a master flat or not.
One thing to keep in mind is that flats are divided and darks are subtracted so it is a different mathematical operation.
I must say though in my experience as I have done flats without bias the difference is not great but there is a subtle improvement when a bias is correctly done and subtracted from the flats before using them.
"
For the flat divide to work properly, the camera's bias (or pedestal) must be
removed (subtracted) from the flat prior to flat fielding (normalization and
division), otherwise the flat fielding will under-correct (e.g. vignetting or
dust donuts will not be completely removed). There are 3 ways to remove the
bias:
1) Dark subtract the flat as if it was a normal exp (in fact it is).
or
2) Subtract a Bias from the flat (instead of a dark). Flat exps are commonly
very short and there is not enough time for significant dark current to
accumulate (e.g. there is very little difference between a 2 sec dark and a
bias). What little difference there may be (between dark and bias) is totally
insignificant due to the flat's high intensity, which completely buries any dark
current. This is very convenient because you can create a high quality bias
(e.g. made from 30+ frames) once and use it repeatedly, regardless of flat temp
and exp time.
or
3) Subtract a constant (equal the avg bias level) from the flat. This usually
works just fine unless the cameras has a very strong bias pattern and the flat
is very weak.
Stan
http://www.stanmooreastro.com/"
I suspect the above is more important if you have a lot of dust donuts in your image or if your camera is pretty noisy or if your cameras' bias pattern drifts around and is not stable.
Greg.
.. slightly obtuse perhaps 
but not rude 
