Symptoms
Agentless scan results differ from an Agent's scan results even though they are using the same scan template.
Cause
A custom scan template was setup to use the criticality filter.
The criticality filter is ignored by agent scans, this accounts for the difference in scan results between the agent and the agentless scans using the same template.
Criticality is the user supplied threat and severity level associated with a particular vulnerability, this is not the vendor criticality. Most likely these user criticallity levels are not being set by the user so it causes discrepensies in the filtered scan results.
Resolusion
When creating custom scan templates for use in both Agent and Agentless scans leave the criticality setting to scan for all.