🚀 go-pugleaf

If it's not too much trouble for you, I would test one more thing:
In both version 1 and version 2 of the document you examplified,
temporarily remove all graphics and create a PDF. If the file sizes
becomes nearly equal, then you *know* it's the graphics and
not something else in the files or the setup.

Are you by any chance copying the graphics into your documents,
rather than importing by reference? I don't think this should
matter when it comes to PDF file size, but it certainly matters
for the FM file size and stability. You said:
"We were recently unable to create a PDF because the sections
 of the book were much too large. We resolved this by changing
 all graphics in Version 2 from JPG and WMF to GIF."
Copying graphics and letting the troubles that causes you to
make a decision to change the graphics' format is not something
I would recommend...

And, the type of graphics (bitmapped or vector, color depth, etc)
and how the distiller is set up to handle them is a major factor
in PDF file size. Since it seems you do use different types of
graphics in the two versions of your files, then my guess is
that's the reason for the different PDF file sizes.

(Note: it's not the file format per se that causes different results
in distilling. A TIFF or PNG or GIF file format won't matter, as long
as the images really are the same. But GIF only supports 8-bit
color depth, so a 24-bit TIFF may contain much more information
than an 8-bit GIF. And a vector WMF file is certainly not the
same as a bitmapped TIFF file.)

-- 
/Thomas Michanek