It turns out that the following procedure was able to correct the problem:
- Add the affected caches to a Virtual GPS list.
- Click the "Export" button
- Select "Build GPX"
- Make sure that the "Use corrected coordinates" option is selected
- Make sure that the category to which the affected caches belong is included in the subset that will be actively refreshed (or just select "Refresh all corrected coordinates" to be sure).
- Wait for the job to finish
- Refresh the Map Bookmarklist page
The above procedure did the trick for me. How the "S 00° 00.000 and W 000° 00.000" entered these two caches in the first place remains a mystery. But it is not worth investegating if I am the only one who has come across it and a workaround is available.
EDIT: If anyone know a quicker and/or less resource-demaning method for refreshing corrected coordinates (NOT user-note based) than the one described above, let me know in this thread.