2 yurtesen:
It may well be cpufreq WILL fail on some (unsupported) architecture. And the investigation you started is generally a good thing to do. For example, right now I have some issues with pppd and cannot get any feedback on my problems so the only options I have is to negotiate the developers or to dig through OS source
Now, 2 ephemera:
This is an OT actually, but as the topic is closed by now (is it?), I may try:
nanosleep is a function. How it is implemented, you do not know. Who knows, maybe it is doing some funny things with the CPU, so there is no guarantee that after it you'll get the needed result from rdtsc. Of course, this is a mere guess