To confirm, are you plotting directly to hardcopy (paper) or to DWF or PDF? I've run into a variety of issues with PDFs from text being cut off, to parts of the page missing to blank sheets missing completely on a batch plot. If you were plotting from DWG to PDF, try DWF..... you can always plot a DWF to PDF using a PDF driver to get a more desirable result.
Sounds like you checked everything in the page setup (layout, CTB, etc.)
A workaround that I found useful was to get one sheet to plot correctly and save it as a Page Setup. Assuming all the other drawings within the SSM (Sheet Set Manager) were created with the same template, so very likely all sheet borders/title blocks are in the exact same location (coordinates), otherwise this may not work.
Enter Publish to open the dialog box and drag/drop all the drawings you need to plot, including the one with the "good" Page setup. You can drag/drop the drawing files from Windows Explorer into the Publish dialog box.
Once you have all the drawings that you need to plot (i.e.: the 50 drawings you said earlier), you can then IMPORT the "good" page setup into all the drawings you dropped into the Publish dialog box. Once the imported page setup is applied to each sheet (you can use the control key + a) press PUBLISH.

I have had great last-minute success with this approach whenever there was a plotting issue where something was just not working correctly. Give it a try, good luck!
Chad Franklin
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