@Cranktrain Thanks for getting back to us, very glad to hear you've figured it out!
Cranktrain I'm a bit confused, because I've checked my git history and while I can see that I did add
https://github.com/EsotericSoftware/spine-runtimes.git?path=spine-unity/Modules/com.esotericsoftware.spine.urp-shaders#4.1
to the manifest, I still ended up with the 4.0 version remaining?
Oh dear, this does indeed sound like a nasty issue to track down, good catch and thanks very much for sharing your insights! I assume that the Unity Package Manager does not view a changed source git URL as a reason to update a package as it would when the minimum version number would change to something higher than what it already has downloaded.