The full title of KB 945425 is "Lines of code may be missing if you compile a solution that has a complex project structure in Visual Studio 2008". They are not kidding, you need a complex mix of at least 5 projects, some of which are referenced by both file and project to trigger this.
This bug is intermittent and can be identified by examining the IL or by noticing the breakpoints are automatically moved without reason.
Fortunately the workaround is easy, simply use project references whenever both projects are in the same solution. This should be done anyways as file references are notoriously unreliable when doing a command line build.
This bug was originally brought to light by Kathleen Dollard.