Per the following documentation, step 2, bullet 3: http://confluence.jetbrains.com/display/TCD7/NuGet+Pack
- Specify base directory, where the files defined in the nuspec file are located (the directory against which the paths in from nuspec are resolved, usually some bin directory). If left blank, TeamCity will use build checkout directory as base directory.
You may try adjusting this setting to the root of your project (theoretically the same location as your nuspec file), rather than the build checkout directory (default).