SecureAPlus has a different certificate list. The default setting for SecureAPlus is to trust the certificates that are in its trusted certificate list, which is different list from Microsoft Certificate store.
Therefore, even though a program is signed using a certificate that is trusted by Microsoft Certificate store, but if the certificate is not in the SecureAPlus trusted certificate list, SecureAPlus will block it from running.
To tighten the security measures, we can even turn off the "Trust based on Digital Signature". This means that the program will be trusted by the hash only. In this setting, regardless whether the program is signed, it will not be trusted, until it is approved to run.