I have actually solved this problem but it was a weird one so I will post it and my solution.
I had a movie clip with several children each of which had it's own alpha settings. It also had a bitmap child object with a masked movie clip sitting on top of it.
I was fading in and out the parent movie clip and was getting some odd results all of the alpha settings of the children were being removed and the bitmap was glitching and showing the contents of the masked object that was above it.
The problem was that my alpha value for fully opaque was 100 (as in AS2) not 1 (as per AS3). It took me ages to work this out so hopefully this helps someone else.