I\'m using a Exynos 3110 processor (1 GHz Single-core ARM Cortex-A8, e.g. used in the Nexus S) and try to measure execution times of particular functions. I have an Android
Are you sure governors are used in Android for performance management the same way that in standard Linux? And are you using custom Android image or one provided by manufacturer? I would assume there are lower level policies in place in manufacturer provided image (tied to sleeps or modem activity, etc). It could be also that sleep code directly scales voltage and frequency. It might be worthwhile to disable the whole CPUFreq not just the policies (or governors).
Check out this professor's page: http://users.ece.utexas.edu/~valvano/arm/ He has multiple full example programs that have to do with time/periodic-timers/measuring-execution-time, they are developed for ARM Cortex-M3 based microcontrollers. I hope this isn't very different from what you are working on. I think you would be interested in Performance.c