 <p>This strongly resembles a very similar problem in Visual&nbsp;Studio&nbsp;2008 SP1. It was fixed with a post-SP hotfix. But there's other evidence that the hotfix didn't get incorporated into the code base, this <a href="https://connect.microsoft.com/VisualStudio/feedback/details/556756/debugger-randomly-treats-step-into-and-step-over-as-run-to-completion" rel="nofollow">feedback item</a> was also a problem. It isn't that unusual for hotfixes to not get integrated back.</p> <p>There isn't a feedback item that exactly describes your problem, at least that I can find. I'd recommend you file one. Given the usual trouble with reproduce bugs like this, I'd strongly recommend you include a reproduction project that exhibits this problem with instructions on how to reproduce the issue.</p> <p>There is a workaround of sorts for your issue, you could go into Debug + Windows + Threads, right-click the threads you don't want to debug and select Freeze. Don't forget to Thaw them later.</p> <p>These bugs were fixed again in Visual Studio 2010 Service Pack 1.</p>