If you select multiple processes in the pipeline editor, the calls are chained. The outputs of the first one are the inputs of the second one. Is this really what you are expecting to do?
Make sure you clearly understand the way this batch editor works before trying again:
https://neuroimage.usc.edu/brainstorm/Tutorials/PipelineEditor
It could be interesting for you to script this step, this tutorial would help you:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting
If the comments above do not correspond to your request: please try to describe better your problem.
From your description, I'm not sure I understand what are "ABR", "Lmon", "Rmon" or "Ref".
And I'm not sure the screen captures match exactly your descriptions, or the results you get.