I am not sure if this helps but HOMM4 is protected with SD2.51.xx, whereas Alice has an old sd2 protection (up to 2.30.xx, I don't know the correct version) and Dungeon Siege only uses cdchecks (I think).
Maybe it is a hardware problem, because I don't know of any Philips writer that is able to do correct efm encoding and not all dvd drives can read in raw-dao(96) mode.
I cannot give you any hints in the right direction as I neither own the game nor the latest version of clonecd (still using 3.3.4.1).
Try to look
here to get the right settings for clonecd.
Hope this helps.