Hi,
Thanks for your replies, sorry for not making it clearer what the issue was. Previously before the error began we wouldn't have to set up an alpha element as it would appear automatically in the frame buffer when rendering (this is still the case.) However what has changed is when the render has finished and it is set to save all of the elements from the frame buffer it will save a .tif (just the format we use) for every element except the alpha pass, which it did used to do. When I hit save all from the frame buffer it also will not make an alpha.tif.
Thank you for pointing out it now loads into the channels, I guess this is more of a bug report as some previous functionality seems to have stopped working.
Matt