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 have had the same problem with MS Visual Studio 2008 SP1. PDB files matched executables files, so it was not a problem.
The problem was Visual Assist
. I turned it off in "Tools | Add-in manager" and after that there have been no problems with skipping breakpoints. So turn off any add-ins that you have in Visual Studio and install latest SP (it is SP1 right now).