When choosing to download your search results in raw-data (fastest) mode (1st option in screen shot below) NetSuite is not able to communicate the order of the columns to CloudExtend. Most users end up building pivot tables and charts off the raw data making the order unimportant anyway.
If the order is important we suggest building an Excel macro that you can run after the download that will change the sort order to the one you prefer.
Pro tip -> Macros don't have to be coded. Learn how to record them here.