Please can you explain why this is the case? - I can see what you are doing and that you don't want it change your method of doing this (i.e merging and unmerging) but getting an idea of why you are working like this might allow an answer that can give you a slight suggestion on tweaking your process.
While looking to answer this for you, i can see that excel counts a merge cell as one (which is probably what you have noticed) so it will not double count a merged cell, even if it covers a range of 2 cells.
I have added the image of what i think you have and the totals at the bottom. The totals at the bottom don't currently show what you would want.
A bit more information would be handy.
