Hi , I did get a new laptop. The old laptop was Linux , the new one is Windows. My custom software read the Intel hex format file and boatload my device. In Linux it work 100%, but in Windows not at all. The hex file size differ as well. At the end my problem was not so big after all. But hours later, I see the Windows Intel hex format file has a "\r" char before the "\n" char in every line, Linux does not have the "\r" char. So after removing the all the "\r" chars in my read function of the Intel hex file, my custom software work again. If you do a compare the file's look the same, but it is not the same.
Maybe it helps some one else. Enjoy your codding.