Good resources to learn about MSBuild and Continuous integration with TFS

Continuous Integration From Theory to Practice by Carel Lotz. It covers the entire scope of your problem, and then some. Well written, complete, and a full sample are all there.

Hands down best resource. Use it as a tutorial first, then use it as a guide, then use it as a reference.

MSDN and others are good for clarifying (or confusing) the details.

Edit: The guide by Carel Lotz uses MBUnit for unit tests (see his earlier document version for NUnit, though you can replace the MBUnit with NUnit pretty easily if you follow the NUnit help files).

Also, it is written to use Cruise Control.NET to run the MSBuild script in various configurations.

Personally, I run unit tests in a secondary MSBuild script, but have found that wrapping the NUnit calls in MSBuild gives more flexibility than running from CCNet directly.

If it's for CI then you're most likely doing an Incremental Get. TFS will only bother to get files it thinks have changed since its last get - e.g. if you delete any files from your server, it will still think you have those files so it won't get them again. In this case you'll need to run the build once with the incremental properties turned off so that it forces a full get of the source. You can do this by overriding the properties in the MSBuild command line box in the Queue Build dialog with:

/p:IncrementalGet=false;ForceGet=true

Another possibility that springs to mind is that the Label task is confused by your branch. It may be that your workspace is set up incorrectly, so check that you're mapping in everything it needs.