Hi Sam,
Normally, tests that aren't run should be shown in the HTML report generated by the console tool. It's possible that tests weren't run by the tool if the tool is using an engine mode or automatic execution filter that excludes the tests from the run, or if the tests are making use of RequiresCapabilityAttribute and the machine running them doesn't have the appropriate capabilities declared in its configuration.
The tool returns a separate return code for when tests were missing from the run, because in many situations this could be considered an error case that people would want to consider (for example, if the tests were dependent on there being a connected grid node that happened to be offline). There is no feature in the software itself that can tell it to 'ignore' such a state and return 0, but you could easily wrap up the tool in a batch file that would check the return code and return 0 to your CI system if it didn't pass a simple condition.