Hi @Nibba, welcome to the forum!
From what you describe it sounds like AFO doesn’t know about your vaults yet. If this worked before but doesn’t anymore than my guess is that “before” means pre-Release 2024.1 (macOS & iOS) – in this version, the vault handling changed. I think that’s the case because you wrote:
However, the vault was specified in the shortcut and the pop up window did not provide any options to specify a vault so I had to give up.
Just re-run the onboarding (“Link your vault”) for all the vaults you want to use with AFO. Then, check the workflow in the Shortcuts editor again, click the Create Note’s Vault parameter, and at that point you should be able to select any of your linked vaults.
Let me know how it goes!