Hmm, autotune on windows is super inaccurate at the moment. The gettimeofday() routine I am using on Windows seems to have a resolution that is not accurate enough. And I think I skip the "take 3 measurements and average" policy when in scrypt-jane mode... But it is not a good idea for low n-Factors...
This needs to be refined before a new release.
Christian
Have you tried using:
SYSTEMTIME time;
GetSystemTime(&time);
WORD millis = time.wMilliseconds; etc.
for Windows?
I think it is the most accurate one