This sounds strange. The ca.cer of your Toniebox Backup must not be copied to the server folder of your Teddycloud instance. Your Teddycloud has its own CA certificate which has been generated upon the first start and this is also the one you have flashed/replaced on your Toniebox (hopefully).
The original three certificates of your Toniebox only have to be copied to the client folder of your Teddycloud instance!
If your flashed Toniebox has another ca.der in its flash than your Teddycloud instance in its server folder, it‘s no wonder that they can‘t communicate with each other.