[spdesign]

It looked as though bootstrap css was being pulled in after theme.css.

After double-checking to make sure I had set developer_mode to "On" in config.php (check), making sure everything was unchecked under Look & Feel > Performance (check), and making sure theme.css was not being served in an aggregated state (check), and emptying browser cache repeatedly, some color instructions in theme.css were still being ignored in favor of color specifications in bootstrap css.

I manually deleted all cached files in /var, and now it appears that theme.css overrides bootstrap css as it should. I'm not sure if that's what did it or it was coincidental to some other change, but it's OK now.