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I would search your Apache access logs for instances of dispatch=payment_notification.return and see if you have some successes or whether it's all failures. If all failures, then I'd assume you have an ownership/permissions issue on your site. But the access logs will probably give you more detail.
The dispatch=payment_notification.return should define('PAYMENT_NOTIFICATION', true) and then call app/addons/paypal/payments/paypal.php. So odds are that it is the reference to paypal.php that is actually generating the 404. Check .htacess as well as ownership/permissions of all directories/files in the path.
I have the same issue, while everything was working fine, about 4 days ago all successful orders started coming in as "open" I am running CS Cart Version 4.3.3
When I check with the hosting provider, below is their response ---
It appears the command PayPal provides is OS specific. The one provided uses cert directory locations for possibly an Ubuntu system where your VPS is running CentOS. When omitting the " -CApath" option the command executed successfully and returned an OK:
This shows it's not a server configuration or an SSL certificates. This leaves be to believe it maybe an issue with CS-Cart and the way the URL's are provided causing the redirect issue when PayPal attempt to connect.
Without omitting the "-CAPath" option the results were
New, TLSv1/SSLv3, Cipher is AES256-SHA256
Server public key is 2048 bit Secure Renegotiation IS supported Compression: NONE Expansion: NONE SSL-Session: Protocol : TLSv1.2 Cipher : AES256-SHA256 Session-ID: 9E01CD86FA9D5CB1AD505F17E34C0D9B92D9C7A09AF2BC0BF2946F88585CE9E2 Session-ID-ctx: Master-Key: 9CF1EC6B3F6ABDB3D2EC7076DCEC56106C23778389F8FE20047702B383AC79CD65F958C13 Key-Arg : None Krb5 Principal: None PSK identity: None PSK identity hint: None Start Time: 1461568996 Timeout : 300 (sec) Verify return code: 20 (unable to get local issuer certificate)