Hi,
The SonarQube Scanner execution fully relies on the Java stack for any SSL matter. And your error here is indeed a sign that some custom certificates are not trusted by the local Java install.
For any SSL-related error that remains mysterious after a first investigation, I would suggest the following tricks: Oracle guide on debugging SSL/TLS connections , using javax.net.debug. This can help understand in details which truststores are in use and why the handshake fails.