Hi,
There are two possibilities here:
1. You have a build task that is creating a console window when NCrunch builds your projects
2. You have test code that either directly or indirectly causes the creation of a console window
To tell between these two, try running NCrunch in the 'Run all tests manually' engine mode. If the console windows keep showing up after resetting NCrunch, this means that the problem is in the build system (which is probably harder to troubleshoot).
If you don't see the console windows while NCrunch is building in manual mode, this means it's happening during execution of your tests. It should be possible to identify which tests are causing the problem by selectively running them in groups, narrowing the problem down until you know which test(s) are responsible. You can then examine them in more detail (perhaps using the debugger) to understand why they are creating the console windows and whether you can change their behaviour.