Suspected sync issue while starting application from Qubes menu

[gonzalo-bulnes]

May not be entirely relevant (seems to be the other way around in relation to what you need), but your question reminded me of this answer about another VM startup race condition:

Can I make VM A start every time I start VM B?

Yes, I forgot about that: As a workaround I always add the line /etc/qubes-rpc/qubes.WaitForSession in rc.local before the first qrexec-client-vm command in the script.