Seems recently our server has been marking more incoming emails as spam
 

So gmail or what ever coming into the server is getting higher spam ratings.
Even emails from one domain to another on our server.

Not sure if we can update or change a setting to check why this happened?

ISPCONFIG is Version: 2.2.12

You should update your ISPConfig version to the latest release to get a current version of spamassassin.

For details on the spam scoring, take a look in the email headers of the emails marked as spam, you find the relevat tests and scores there.