Had the same issue, and fixed it by changing the configure.php file in the /catalog/includes/ folder.
Bottom line is that if your store is in a subfolder, then the server define should include that subolder spec, but the catalog directory defines should all be just /catalog/.
Code:
define('HTTP_SERVER', 'http://www.mystore.com');
define('HTTPS_SERVER', 'https://mainstore.biz/mystore');
define('ENABLE_SSL', true);
define('HTTP_COOKIE_DOMAIN', 'mystore.com');
define('HTTPS_COOKIE_DOMAIN', 'mainstore.biz/mystore');
define('HTTP_COOKIE_PATH', '/catalog/');
define('HTTPS_COOKIE_PATH', '/catalog/');
define('DIR_WS_HTTP_CATALOG', '/catalog/');
define('DIR_WS_HTTPS_CATALOG', '/catalog/');
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