Batch plotting (the command PUBLISH) of all layouts (drawings) uses very wide page margins in the resulting PDF file - the plotouts are unusable. Individual, single plots are OK. You are using Acrobat.
The cause is probably that you select the "Adobe PDF" printer for your single plots. But for publishing, you select the "Publish to:" option set to "PDF":
But this option makes use of the AutoCAD printer driver named "DWG to PDF.pc3" - it may have different margins defined from the margins set in your Adobe PDF printer driver.
So either set the "Adobe PDF" printer as the default in all layout sheets and then choose the option "Plotter Named in Page Setup" for publishing, or change the page size and margins in the printer driver "DWG to PDF.pc3" (see e.g. C:\Users\*username*\AppData\Roaming\Autodesk\AutoCAD 2013\R19.0\enu\Plotters).
We recommend to always use the printer "DWG to PDF.pc3" for printing to PDF from AutoCAD - this internal printer allows to embed layers into the PDF (usually cannot be done with external printers) and avoids frequent problems with drawing orientation on a sheet.