Installing BenchMate 0.10.8 or higher will automatically fix this problem by advertizing a higher QPC frequency so BenchMate thinks HPET is enabled. Internally it's just another scaling factor.
For older versions of BenchMate you can fix this warning by setting the timer for GPUPI manually in BenchMate. Right-click the affected GPUPI version in the BenchMate client's launchpad, go to "Options/Tweaks", "Timer Emulation" and select "Driver". GPUPI will now use HPET by default.
This warning should only happen with GPUPI 2.3.4 or yet untested hardware, because the automatic Timer Emulation of BenchMate is not working properly.