uploaded and downloaded *.pof file are binary different

Hello, I'm working with Quartus II 12.0 and MAX II CPLD. When I'm uploading a *.pof file via USB-BLaster (JTAG) and then directly afterwards examine this file and save it to my harddisk, they are binary different. My first Question is Why? My second Question is, can I convert a downloaded File in a comparissionable format? (how?) Many thanks for possible help. Marm