So how are you launching the renders now? So it looks like the quality changes on mental ray change nothing in the batch render? Check if this is true in other maya scenes in case you have changed something by accident thats effecting all batch renders.

The solution with pasting the plugin files into the batch render packages sounds like its on the right lines, generally rendering is done externally from the main package so if you want plugins to work in the batch the renderer needs access to the plugins used in your maya scene.

Then again it could just be maya isn't telling the plugin to load, might be worth reinstalling XFrog to see if it correctly installs all the libraries / shaders it uses. These are meant to be shared with batch but something may have gone.

If you want to get to the guts of this upload the log somewhere, there will be a line somewhere, cant find x skipping object X.