Build.net does not detect all file changes.
 

When I update a certain header file it should cause several items to build when it is changed. But when built by visual build it does not detect the change like 2005 does.

Is there anything I can do to force it to detect the change?

Even when built from VBP, it's still VS/MSBuild that actually scans dependencies and determines what needs to be built for a VS project/solution. Building via devenv rather than MSBuild might help, but even that is not necessarily identical to building in the IDE.

If that doesn't resolve the problem, you would need to contact MS support regarding the issue. You can check the 'Display compiler command-line' checkbox on the Options tab, rebuild, and copy the command-line used to reproduce outside VBP and provide with your support material.