Hello Moshe,
You need to import the whole chain of your new certificate into the STRUSTSSO2 transaction (SSL Server Standard). With "chain" I mean your new certificate and the Root Certificate, the validation of the certification goes through several levels that has to be checked:
-> Root Certificate (SAP CA Certificate).
---> Your new server SSL Certificate
It is not possible to authenticate the certificate if you don´t have the root certificate installed.
Regards.