I have the same problem, and all my layers in the same projection. It appears that a problem occurs where one of the rasters has 'null', the tools then just assigns 'null' to that point for all other rasters which are below it onthe list of input rasters. Very frustrating, I don't have a fix yet being carefully choosing the order you put your raster layers into the tool, but this can't always work when differnt rasters have different areas of missing data!
Please ket me know if anyone has a better idea.