Hi,
Without more information, I would point out that you probably are missing data from repeat groups in what you are seeing on the CSV. If that is the case then you should know that the CSV will only show you data from one sheet of an excel. On the other hand, when you export data from repeat groups, this will be located in separate sheets from the main sheet (which is what you had in the CSV. My suggestion would be you download the data in XLS and not CSV if you have repeat groups in the form. See this previous discussion thread
If the issue is not as I had indicated above, could you please provide more detailed information.
Stephane