Currently, due to some optimization, Vertex Groups that are not used in the modifier stack are discarded for the object's evaluation. This brings up the issue, that when an object is referenced in another object's node-tree (Object Info / Collection Info) every vertex group that is not flagged as being used by that object's modifier stack is not propagating along with the geometry.

Current workaround is to explicitly add a modifier that flags the needed vertex groups as needed or add an empty geometry nodes modifier, which automatically does that for all vertex groups.