Hi, thanks for posting!
The auto node selection happens when no existing nodes are selected in the list, and the list is then updated by NCrunch. The main use case would be if you had an empty list of tests/projects, then made a change that caused one of them to fail and appear in the list. You'll probably never see this if you have the 'Show passing tests' option turned on, as you'll end up always having something selected.
It would be great if you could share some more details about whether you see a more intuitive way to handle this. It's a new feature, so I'll accept that it may need some fine tuning.
Cheers,
Remco