When starting the NUnit GUI from the command line, you can specify a configuration. If you are doing this with a solution instead of an individual project, it does not work correctly. It assumes that all the projects have the same configuration name as the solution configuration. While this is often true, it is possible to have a solution configuration that uses project configurations of a different name.
If you need more detail, this is how I have my project set up in Visual Studio 2008. I use the Configuration Manager under the Build menu to organize my configurations. I have a solution configuration called "Test". Some of the projects under this solution do not even have a configuration called "Test". For these projects I have the "Test" solution configuration using the "Debug" version of those projects. When I load the NUnit GUI using the command line and pass it the location of the solution file and instruct it to use the "Test" configuration, it only loads the projects with a configuration called "Test" and therefore is ignoring the solution configuration settings.
The /config option refers to configurations stored in an NUnit project, which may or may not map to VS configurations.
When you open a VS project, NUnit creates an in-memory NUnit project, which includes all the configs found in that project. This is usually what is wanted, but if you required something different, you could edit the config and save it as a .nunit project file.
Similarly, when you open a VS solution, NUnit creates an NUnit project, which includes all the projects found in that solution whose project type is understood by NUnit. As you noticed, it's just the union of all the configs in all the projects used.
I agree that it would make sense for NUnit to use the config information in the solution file. I'm characterizing this as a new feature we should try to get into a future release.
In the meantime, I suggest you open your solution and save it as an NUnit project. You can edit the NUnit project by hand or in the project editor to get the configs set up the way you want.