You might try the RS=NONE option in your invocation
filename mvsfref 'www.xxx.yyy.zzz';
ods tagsets.excelxp file=mvsfref rs=none;
I don't know whether it will help with ExcelXP -- but it's specifically recommended for cross-platform creation of HTML files because RS=NONE specifies that every line gets written out one at a time to the file, with the appropriate carriage return/line feed character at the end of every line and thus, there is no awkward wrapping that might get truncated or messed up by FTP. Since XML is a markup language text file, like HTML, it's worth a try.
The other thing is to see if it makes a difference to FTP as TEXT. Otherwise, you may need to contact Tech Support for more help.
cynthia