I have almost the same issue. My downloads work well on xls format. The parent data (the household information) and the repeated data (some household members information) appear in different sheets.
However, when I download in CSV format, it sounds like the repeated data is ignored. Only the household data (parent) and other non repeated questions (closing questions) are downloaded.
Is this issue known i=or is there anything I missed.
As I said, I am getting around the problem by downloading the data in XLS format but I would like to know if there is a solution to the problem with CSV.