I am having difficulty converting my PDF file to Gerber. The PDF consists of the same image stepped out over a 12" X 12" panel.

Not every PDF/Postscript file converts cleanly (in fact PDF/Postscript files are similar to the complexity of converting DXF files) so many times some tweaking is necessary:

1. Try producing a 1-up image in the PDF file. ACE has editing abilities, so you can then Step & Repeat the image after loading into ACE.

or
 
2. In ACE Viewer, try cleaning up to resulting gerbers before export. ACE has some excellent features & tools to clean up data before exporting.

or

3. Output the PDF/Postscript from as a large monochrome bitmap using graphic tools like Adobe Illustrator (which can output bitmap images to any resolution), or the freeware tool called "The Gimp" which can import any PDF/Postscript and output a high-resolution monochrome bitmap.  Once you have this, you can easily convert it to gerber or ODB++ using ACE (select "Large Bitmap" as the import format).  We would recommend in these cases to uncheck "Output Pixels as Flashes" (in Larger bitmap import).