I wouldn't take the queue messages in the log too seriously. The console tool is an adaptation of the NCrunch engine designed to run without a UI, and as such it has a workflow logic that reflects a situation where state changes made to the engine happen progressively through the run. I suspect in this case that the tests are being queued before all the configuration gets applied, and they then get removed from the queue later.

The log output from the console tool is a very internal view of the workings of the engine. These logs were initially designed for us to troubleshoot the engine itself, as opposed to being a user-friendly way to examine the workings of a console tool run. I guess this is just the way that things have progressed that these logs are now very visible and being used by everyone to understand what the console tool is doing. The root problem here is that the workings of the tool are not descriptive enough for anyone to understand how it behaves and why it does what it does. We just haven't put enough investment yet into the reports to be able to show this sort of thing, but we're working on that :)