I mean when you get a .patch file and git-am that doesn't provide the same associated info (or environment) for git to resolve a merge.
Knowing that, it is very strange that the two methods should yield different results: the patch file is supposed to rely on a parent commit that should be accessible on the local repository, just like a local series of commits. That somehow the associated info/environment differs indicates there's a bug somewhere —or at least yet another poorly thought out corner of the UI.