If you are getting 403 error on your site with following messege in your error log
Permission denied: /home/user/public_html/subdomain/.htaccess pcfg_openfile: unable to check htaccess file, ensure it is readable
Then it seems that the nobody user is not getting read and executing permission upto any of that folder.So make sure that the public_html and the subdomain are set read and executing permission.
If its not set then change it.
That will fix your issue.