My apologies for the slow reply. I have been on vacation.
The analysis function I used works best with at least ten cycles of the
waveform. If you don't have that much data, it could introduce
inaccuracies. If this is your problem, try increasing your number
of data points (if you can). Averaging is also an option.
Whether you take a measurement each time and display it or average
several measurements and display the result depends upon what you are
trying to accomplish. There is no right or wrong general
method. If you don't mind the jitter in your display (which, as
you mention, may be real), use single measurements. If you do
mind, average. If you average, I would strongly suggest that you
at least show some statistics (max, min, standard deviation) as well so
you don't hide something you really should know. You can also do
both (raw data and average data with statistics).
Have fun.