Hi Eli,
No code was being written to the .htaccess file. The file was being replaced every time I tried to update it manually or via the WP interface. The issue mysteriously disappeared just like when it mysteriously started exhibiting the issue.
I think because the site is on shared hosting that there were other issues behind the scenes. There was also an issue with the PHP version that the host said was affecting other sites too.
I've cleaned it all up and all is good now.