Rob, thanks for the help.
The categorylinks table was empty after the operation. Editing and saving a page creates a row in this table. Then that page is listed on the category page. So the categorylinks table seems to be working.
There were no error messages during refreshLinks.php, just the progress indicator.
Maybe there is something in my LocalSettings.php that is incompatible with the maintenance script. Or some other enviromental issue...
If nothing else works, maybe I'll try the same database with a new installation of the MediaWiki software.