I thought suspend/resume as well as long running Templates should be improved by modifying qvm-sync-clock for Qubes-Whonix. Started working on it:
Not in use yet. And was probably in vain. And probably low priority.
Because…
Then if this “small” difference is causing some much issues… The reason for that is probably:
If someone would like to try if that is the case, try the workaround of disabling boot clock randomization.
Related boot clock randomization development discussion:
Boot Clock Randomization - bootclockrandomization