Hi Magnus
    You are right, I could compensate it in the software. I've tried that.
The software sets sig=ref=10MHz and measures start-to-stop time t1. Then,
it sets sig=ref=5MHz and measures time t2. With t1 & t2, I could get the
time difference between the start path and the stop path. Repeat it 1000
times every second and get the RMS value of it. I use the RMS value to
compensate the result of the following second, but get much worse ADEV
chart.

    I've uploaded the verilog code and schematic to
http://www.qsl.net/bi7lnq/freqcntv4/code/freqcnt_v4.zip and
http://www.qsl.net/bi7lnq/freqcntv4/freqcnt_bi7lnq_v4.pdf.
    The idea is from http://n1.taur.dk/permanent/*frequency*measurement.pdf
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