It seems that R# is running TestFixtureSetup and TestFixtureTearDown on test-fixture classes with an ignore attribute:
[Ignore("These aren't ready yet")]
public class MyIgnoreTestFixtureClass
In our case, our TestFixtureSetUp method should NOT be run but is, and is causing an exception which in turn is causing the tests to fail. This behaviour is different from nunit-gui which doesn't run the TestFixtureSetUp method.
Hope this helps.