Scheduled WebI doc is not generating .csv format file for report data, but creating csv file with data providers (queries) data and its behavior of Webi report from beginning. Meaning CSV format always generate complete data providers data not the formatted / calculated report data. Save As/Schedule to CSV will give the raw data of data providers; whereas, Save As Excel/PDF/Txt will give the report data.
You can achieve this when you upgrade to BI 4.1. In 4.1, scheduler has “Plain Text” which will give you report data as expected.
There are some workaround to convert Excel file to CSV using VB macro.
DWBI castle 