I am running Visual Studio 2008 with SP1. When I debug an application, it will skip over my break points.
For example, I have two lines of code, each call a method.
I had this problem and had to install a hotfix. See http://social.msdn.microsoft.com/Forums/en-US/vsdebug/thread/f3fcb4fb-8a08-4fa0-8d58-9ed6f3eb1193 for details