When I run my NUnit tests, I don't create a XXX.nunit project file. At the console I type:
nunit-console.exe c:\myproject\bin\myproject.test.dll
In your case, you have a .nunit file that list the assemblies to test. Make sure the paths in the file are resolving correctly from where you are executing nunit-console.exe. My example has the full path to the assembly so I can run nunit-console.exe from any where.
The nunit file looks something like this:
<NUnitProject>
<Settings activeconfig="Debug" appbase="C:\dev\Community\src\" />
<Config name="Debug" appbase="C:\dev\Community\src" binpathtype="Auto">
<assembly path="Profile.Test\bin\Debug\Profile.Test.dll" />
<assembly path="Roster.Test\bin\Debug\Roster.Test.dll" />
</Config>
<Config name="Release" binpathtype="Auto" />
</NUnitProject>
The appbase setting indicates where to fine the assemblies to test. So the full path to the assembly is appbase + assembly path.