I've got the same problem and wasted a couple of hours to figure out what the problem is.
In our case, the NUnit plugin was configured to run the tests from:
**\*Tests.dll
Though this sounds to be OK, it has turned out that this pattern will not only match to the MyTests.dll in the bin\Debug folder but also to the obj\Debug\MyTests.dll. The obj folder is used internally for the compilation and does not contain the config file.
Finally the solution was to change the plugin configuration to
**\bin\Debug\*Tests.dll
Actually we use a system variable for the build configuration so we did not have the "Debug" hard-coded. Using bin* might be also dangerous when the workspace is also used for Debug/Release builds and you don't have a full cleanup specified.
You might wonder why I did not realize the test count mismatch (actually it was doubled, because they were running once from bin and once from obj), but this is typical: while everything is green, you don't care about the count. When we have introduced the first test depending on the config, we had only one failure (because the one from bin was passing), so the duplication was not outstanding.