What is annoying in the create replica of the �??distributed deodatabase too bar�?� is that all feature classes are required to be added to the table of contents to create a replica for them.
I couldn't agree with you more, which is why I keep a saved map document handy in cases where I need to re-create a replica with the same data from time to time.
In terms of why the GP tool might be experiencing failures compared to the toolbar in ArcMap completing successfully, that might be a bit difficult to uncover. Are you running the GP tool as part of a model or independently?