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The LPF would not cause drift. Drift is related only to the 27MHz Si5351A reference oscillator. 20m is the first transmission after your calibration pause. Things I would try myself:
1) Take a look at http://www.qrp-labs.com/synth/freqstab.html just to be sure you did everything it mentions there. I don't think you put a heatsink on the 27MHz crystal. That can be useful sometimes. An old nut glued on is good enough. Here, I find any suitable small piece of metal around the workbench and glue it on with epoxy.
2) You mentioned that your frame contains only 30 seconds of non-transmit time. Of that, you have your calibration set to run for 10 seconds. Calibration is done at a much lower frequency, where the microcontroller is able to measure it. That means that the synth will only operate at the Park Mode 2 frequency of 150MHz for 20 seconds. Probably it is not enough to heat the Si5351A up enough. I suggest increasing your "Frame" parameter, add 2 minutes to it. Then The Si5351A will have 2 extra minutes at 150MHz "Park" to stabilise itself.
3) Try Park at 150MHz, and try it at a much lower frequency e.g. try it at 14MHz (same as transmit frequency). What is the drift, in each case? If you find that drift is positive in one case, and negative in the other, then this means that in your particular situation, 150MHz is too high. It is OVER-compensating, heating up the Si5351A too much, so that when you come to the 20m transmission, it is cooling down and drifting. The solution is to try lower frequencies than 150MHz.
I recommend trying these things one by one, not all at the same time. One by one means you will be able to find out which one (hopefully) reduces the 2Hz drift to 0Hz.
73 Hans G0UPL
On Wed, Nov 15, 2017 at 12:36 AM, Vernon Matheson <vmath@...> wrote: