I have just tested it on the local installation and it works correctly.
Hmm. CS-Cart also said I was correct on the fix, but to delete my var/cache folder. I did do that before I asked and it wasn't fixed. Went to different browsers but the pages still ended in html.
Going to wait now till I have time to try again. Had all wrong extensions for about an hour and a half where people clicking through from Google (or anywhere) would land on a 404 error page.
I was able to revert back to previous version to fix it.
Thanks for checking on a local install. At least I know it was the correct way.