you must addecuate both intel-hex files, as some tools make it 16 byte width and others make it 32-byte width,
also some compilers(linkers) build them unoredered (like sdcc) but mostly, readers get them truly ordered...
so I build myself a tool to re-order and make it 16byte width, a long time ago, (just for the same task
) (the sad new is that i lost to source of it, and of course, it's as is, no warrant or anything....)
EDIT: ok, i found the source (I think) checking it, it has an ovious limitation of 64K hex file, the command line should be
hexo [input_file.hex] [output.hex]
no need for extention, but it search a correct Intel-hex file.
attached is an quick example of
after reordering both files, you can compare with a normal text comparition tool...