Um ... The "htaccess that comes with ZC1.3.9g" doesn't restrict robots.txt files ... because there IS NO .htaccess in the root folder of the ZC files, which would be where your robots.txt file is put.
So, it appears that you've copied content from the /includes/.htaccess into a custom /.htaccess file, and thus broke normal operation.
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Zen Cart default does not have an .htaccess file in the 'root' dir. but that doesn't mean you can't have one.
The .htaccess file for example that you provided in your original post is a custom .htaccess file that does go in your Document Root. If you include parts of other .htaccess files though, that are from other .htaccess files located in other directories, it could lead to problems such as you were experiencing.