To be precise, it is still a software issue. The pi has no hardware clock 
.
Anyway, thanks for your help, rossko57!
The Pi lacks a hardware real time clock to keep independent track of time of day. It has of course a hardware oscillator or clock to drive the chips, and system software can derive timekeeping from that. On Pi3/4 the chip clock is variable to control temperature (and add confusion) but its crystal regulated which should give around 100ppm accuracy. I believe the crystal works as a reference, to trim the master oscillator. Broke crystal, master oscillator runs significantly off-spec.
Thanks for the details, I am not that deep in building PC clocks. I will organize another Pi today and give an update today or tomorrow.
I am running out of ideas: I used another Pi with the same SD card and have exactly the same drift. It seems to be some kind of configuration but have no clue what. 
Don’t rule out the potential of the card itself … weird stuff happens at low level storage access.
Try an openhabian setup for a standard environment.
I now have something different in mind. I still have an old line in my boot config that reduced the CPU speed dynamically:
arm_freq_min=200
I think that is not supported since a while anymore and somehow I don’t have a good feeling with it. Trying now…
I think the real thing runs at 250 or 500. Clock time is derived from this, in complicated fashion, so yes a source of timekeeping error.
Jupp, that’s the error. Now it works. Long process but solved. 
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