I've tried using multiple file-ids in the shortcode in my page, but the resulting links do not appear in the same order as they are written in the shortcode. If I specify single file-ids with multiple shortcodes then everything is ok.
I've kept both variants in for now at
The first shortcode is [download id="14,13,8,7,6,5,4,3,9"]
The remaining shortcodes are [download id="14"] [download id="13"]and so on.
I'm using the Weaver II Pro Theme, the same happens using TwentyTen.