There is a known problem with MSBuild whereby it does not cater for database project types as these project types (database projects) are not buildable. This is only an issue when specifying a solution file (as the item to build) within the MSBuild script.
Because these are not buildable projects VS does not show them in the solution configuration manager. Unfortunately this means they cannot be manually configured not to build (as a work around to this problem).
Another simple solution is to just remove the database project from the solution - and if you really want it still within the solution - just create another project of type class library and just reuse the original project's files. By using another project type (like class library) you can use the configuration manager to explicitly flag this project not to build (remember to update each configuration).
This issue affects TFS continuous integration builds.