I assume you are using a 'standard' QRP-Labs synth board and not the
OCXO version.
What Park Mode type are you using Ian??
Examples:? In mode 2 the park mode is inactive during that rather
long calibration time you have, there may not be enough time after
calibration ends and the QRSS starts for the park mode to 'warm up'
the synth again.? In mode 4 the park mode is active all the time
(during TX, between transmissions, and during calibration).? Keeping
the Si5351A 'busy' with continuous park mode activity might help
that 'initial hook' of drift.
Another possibility if the QRSS transmission is the first in the
sequence, is to add a 'dummy transmission' as another "mode" before
the QRSS "mode" (e.g. maybe a CW ident?) to take up the initial
drift hook.
No idea why the transmission might appear to be 20Hz off.? The 20
240 Cal Time setting should set the U3S to within a couple of Hz at
28 MHz ... but now the Ref Freq has settled you might try something
a little finer, like 01 240? (and as above, 240 is longer than is
probably necessary).
73, Bob? ZL1RS