Shane,
There are multiple ways to implement "fill" in the linker command file. You can fill holes in initialized sections and you can fill uninitialized sections. You can end up creating a huge .out file, for the latter, and I am guessing the initialized sections are what are causing the problems, but I need to know exactly what you were doing to understand how it can affect your results.
Can you show the differences between the two versions of your .cmd file?
Which memory model are you using? (-c or -cr, aka --rom_model or --ram_model, resp.)
Regards,
RandyP