COMSIS,
The reason why you are observing different measurements using the Tone Measurement VI and the Timing and Transition Measurements VI is because the way each of those VI's actually work. With the Tone measurement VI, which measures the period of a signal and takes the inverse, it is possible that the funtion misses the actual period by a few samples, or includes a few additional samples in the same period. This creates what is called spectral leakage, which when taking the FFT for a final frequency determinatio, makes it seem as if the FTT is shifted slightly and that is why you seem to be reading a slighly different frequency. Conversly, the Timing and Transition VI, actually counts the rising edges and measures the dt. This is a more accurate measurement because the is no room for spectral leakage to take place.
For more information about spectral leakage please refer to the following links;
http://zone.ni.com/devzone/cda/tut/p/id/4892
http://digital.ni.com/public.nsf/allkb/2A8C234B3F3F4B81862567E60073D997
http://digital.ni.com/public.nsf/allkb/4985224270D324A086256936005879BB
Eli S.
National Instruments
Applications Engineer