Oh, d**mn.
I just had a brainwave.

From Web2c's tex.ch comes the following:

  @!inf_font_mem_size = 20000;
  @!sup_font_mem_size = 2000000;

So font_memory cannot be set larger than 2000000 and not smaller
than 20000. Out-of-bounds sizes are silently folded back in line,
but that happens after the variable expansion is complete. That's
why the debug switch still reports the values from texmf.cnf.

So the actual problem here is the web2c runtime code inside TeX.

You can recompile with a larger sup_font_mem_size, I guess. But
otherwise you are out of luck.

Cheers,
Taco

David Wooten wrote:
Any more clues, patient ones?:

    texexec --pdf file.tex

Here is how much of TeX's memory you used:
1449181 words of font info for 262 fonts, out of 2000000 for 2000

    pdfetex --kpathsea-debug=65535 --ini --progname=context plain

kdebug:hash_lookup(font_mem_size.context) => 3000000
kdebug:variable: font_mem_size = 3000000

Many thanks,
David
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