That's because of backwards compatibility with older versions of excel that can only handle 65K rows.
You can change this with an 'easter egg' setting. In the Help menu select About Qlikview. Then right click on the Qlikview icon in the lower left corner. Find the entry RowLimitForCsvInsteadOfXls. You can then increase the value from 65500 to a higher number. Note, this may cause a performance penalty on your server.