If you are processing on the linux side and not via samba, and your program will take a list of files on the command line instead of groveling through the directory itself, you might simply start it with a wild-card filename on the command line. The shell will sort the list as it expands it so programs see the sorted list.

The processing is done via Samba. Acrobat Distiller is not simply processing a list of files, it is consolidating a group of files onto a single file, discarding repeated graphic objects and creating a single subset of fonts from the various font subsets present on the original pages.

There is a workaround to this: use the runfilex script that comes with Acrobat: it can contain a list of files to convert, in the order you want. Unfortunately, this is not acceptable for us since the process then takes about 40 minutes (irrespective of platform or filesystem), instead of 3 or 4 minutes.

That's very strange. Maybe you should look for a different tool. Won't ghostscript/psutils or OOo do this?
The tools you quote do not apply in this case. I am not talking about office style PDFs, I am talking about full professional PDFs for printing presses, with embedded color profiles such as ISO Newspaper, JPEG2000 compression, bicubic resampling, etc. Not even Ghostscript does that kind of thing. I wish it did, but it doesn't.
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