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.
For web sites, this can occur if a separate instance of MSVS was runnning the same web site.
Just stop the original instance or stop IIS Express.
MSVS seemingly starts the 2nd web site without complaining about the pre-existing one that was running on the same port. Possibly the page shown in the browser is really the 1st web site.