I'm working on setting up a moving-average in the custom C code block that counts the zero crossings to see if this approach is able to mitigate the glitchy frequency readout due to mis-counting by one clock cycle between successive zero crossings. I'm storing an array the size of the moving average window of frequency readouts at each clock cycle, and then taking the arithmetic mean over the window. By keeping a summing variable that updates itself each clock cycle, the actual moving average process isnt very intensive in terms of computational time. The array does take up some memory, but even if I perform the moving average over 1 second with 16384 double precision numbers stored in the array, its still only 130 kB so I don't think it is a concern. Some tests I've been doing while tuning the code suggest that with a moving average over 16384 samples (i.e. 1 second), I can eliminate glitches at the 1Hz level in the frequency readout for frequencies up to 5 kHz (generated digitally using an oscillator block). Some tuning still needs to be done, and the window could possibly be shortened. I also need to take a look at the systematic errors in this revised counting scheme, preferably with an analog source, but this is overall, I think, an improvement.
On a side note, I noticed some strange behaviour while running the cds average command - even though my signal had zero fluctuations, using z avg 10 -s C1:TST-FC_FREQUENCY_OUT gave me a standard deviation of ~1 kHz. I'm not sure what the problem is here, but all the calibration data I took in earlier trials were obtained using this so it would be useful to perform the calibration again.