Re: 5.6.0 breaks deep packet inspection
Can you check what is the name of the CA Certificate that was imported onto your environment? If you have been upgrading your Fortigate from the older OS versions, there's some chance you are using the "Fortinet_CA_SSLProxy" Certificate - it's kept in newer FortiOS upgrades for compatibility purposes.
In FortiOS 5.6, the default profiles for certificate-inspection and deep-inspection uses the "Fortinet_CA_SSL" certificates. If you have been using the default profile while the Certificate you imported previously was "Fortinet_CA_SSLProxy", that would explain why deep-inspection is not working correctly and applications not working.