After our troubleshooting, we found out that the file downloaded by newer version come with empty rows between data, since the .csv files came with spaces (empty rows), it is not being processed and fails.
If a UNIX-newlined text file is read as DOS-newlined textfile, it looks like there is no newlines at all because DOS newline is "\r\n" when UNIX newline is just "\n".
So there is no way of empty lines appearing because of UNIX-newlined file being viewed as DOS-newlined.
Can you provide a small hexdump of a damaged file?
Sorry if my advice was wrong.