It turns out that the "set system sysctl" is runned before interfaces are created which gives that some sysctl cannot be set properly without errors during boot.
A workaround is to set these through "/config/scripts/vyos-postconfig-bootup.script" but it would be nice if the "set system sysctl" could be extended to run some of the commands after the boot have completed.
Suggestion:
Default (or if not mentioned) would be "mode preboot" but changing it to "mode postboot" would be handy:
set system sysctl parameter net.ipv6.neigh.eth3/2.base_reachable_time_ms value 14400000 mode postboot
Another suggestion would be to move when the "set system sysctl" are being runned during boot but that might break other things.
Ref: https://forum.vyos.io/t/how-to-set-net-ipv6-neigh-etha-b-base-reachable-time-in-vyos/14304/4