You should only need one base texture. Forgive me if this isn't the case, but sounds like it might be going wrong because you have more than one layer when you go to make the second recolour (your base texture + the first recolour) - you need to make sure that you only have one layer (the base texture) before you run each action, otherwise you will get strange results. If this isn't the case, then feel free to tell me, and I'll see if I can think of any other explanation!