Thanks for your input, helga. Great suggestion. I went back to functions.php for my child theme and removed all the code I had added. Result: Query is in DESC order as it should be. Then I added in only the exclude_category_five function I mentioned above, and it works as planned (omitting category id #5), but posts are definitely no longer in DESC order. So conflict with other functions isn't the cause. (As an aside, all posts are in the correct DESC order when I check each /category.)
Beyond that, there are no other page templates or additional PHP that I know of in my WP install. It's just Thematic and my Thematic child theme.
I only have five active plugins (Contact Form 7, Contact Form to DB Extension, Really Simple CAPTCHA, Widget Logic and WP Google Fonts), and I'm doubting they're the source of this.
Kind of interesting. Anyway, will explore this further and report back if/when I find the cause.