It is expected MIF file content is not the same when generating the same design on different OS platform. The reason is that content of MIF file for Nios® II processor internal RAM initialization is random data. The seed difference on different OS platform results in different random data.
Example .mif files:
cpu_bht_ram.mif
cpu_dc_tag_ram.mif
cpu_ic_tag_ram.mif
cpu_ociram_default_contents.mif
This information will be added into a future release of Nios II processor reference guide.