I am not sure if this is a bug in orgmode latex exporter or whether it is specific to LaTeX and that there is some code that will take care of this.

First, attached is a copy of my LaTeX setup.

I recently added \\usepackage[npthousnadsep{,}]{numprint} to my setup.

When I export the following in line code

This is inline src_emacs-lisp[:var totalcommissions=TOTALCOM[-1,-1] fmt="%.2f"]{(format fmt totalcommissions)} {{{results(=99999.99=)}}} for some reason

the thousands separator is place above the exported line, thus

    ,
This is inline 99999.99 for some reason

Likewise, a source block, e.g.

** Block

This is a block

#+begin_src emacs-lisp :var totalcommissions=TOTALCOM[-1,-1] fmt="%.2f" :exports results
(format fmt totalcommissions)
#+end_src

#+RESULTS:
: 99999.99

for the same code

exports as

  ,
This is a block
99999.99

{group-separator = {,}

for the same code

Of course I expected 99,999.99 in both cases.

I also tried this with \\usepackage{siunitx} and \\usepackage[group-separator={,}]{siunitx} (numprint separator was removed) and had the same results

Org-mode version 8.3.4 (release 8.3.4 -907-g65e437 @ usr/local/share/emacs/site-lisp/org-mode/lisp)

GNU Emacs 24.4.1 (x86 64 -pc-linux-gnu, GTK+ Version 3.14.5) of 2015-03-07 on trouble, modified
by Debian