I am pretty sure it has to do something with the float values being 'messed up' when they are so small.
Float values do have inherent error involved when they are VERY big or VERY small. The values you showed were neither. Sorry I don't know OpenGL. Where are you getting PCFreq? Is it part of the performance counter? If so, then it should take into account the PC/OS specific values for the clock. Do a check with both PCs. Have your program display the "time between frames". The TBF should be the same on both machines if the PCFreq is the same (or close). If you are running at 60fps on both machines then the TBF should always show ~16.6666666667 (on average). You will most likely see this number fluctuate between 16-17 depending on processor load.
So, to sum up:
Test both computers for 60fps and TBF.