Much simpler approach:
1. Domain Registrar: this is just a domain name, with nameservers set to your hosting company's nameserver values. NO FORWARDING.
2. Hosting company: website is set up to "point to" your public_html/fred/ folder (whatever "fred" is for your flavor of the month folder preference, "store", "catalog", etc)
3. .htaccess - nothing
This way your customers access your site by visiting "www.your_domain.com" and that'll automatically push them into your "fred" folder transparently ... they'll never even know about the "fred" folder cuz that becomes the "top" of the website structure if you do as I described in #2 here.
Granted, I don't usually recommend using a "fred" folder at all, because that just creates all this confusion you're encountering now. If you used no foldername (ie: "store" or "catalog") and none of these "redirects" you're doing, all this mess would be moot.
The benefit of this is no SEO messes.


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