Hey Aflatoun,
I believe I understand your problem. You have a program that you are running on your processor. This program takes about the same amount of time whether your system clock is one frequency or a faster frequency. Is this a good explanation of your problem? I looked at your qar and did not find any software. Based on the simplicity of the software, most of the time taken could be initialization of the FPGA and your system rather than time spent running your program. So it is possible that if make your program more complicated, with more loops, that it will take a longer amount of time. Be careful with this approach though, since the software compiler can optimize out what it sees as useless commands. Please let me know if this doesn't help.
Thanks,
Ben