Integration with NCover not giving the full coverage report

We have a .net exe application for which we have written the unit tests using TypeMock. We use VS2008 and the application targets .net 2.0 runtime. The unit test project targets .net 3.5. We are using Typemock 5.3.

We want to get the coverage report using Ncover, for which the following command is used:

"C:Program FilesTypemockIsolator.3TMockRunner.exe" -first -link NCover "C:Program FilesNCover cover.console.exe" //x "c:coverage.xml" "D:NUnit.4.7in unit-console.exe" "D:TestCodeBuildsUnitTestsinDebugBuildsUnitTests.dll"

Running this command gives the coverage of only the BuildUnitTest code, it doesnot give the coverage of our application code.

Question: What command should we use to get the coverage for the application code?

Note that we use the TestDriven.net to get the coverage from within the VS2008 IDE and that gives the coverage of the application code.

Please let me know as soon as possible as we are blocked by this.

Thanks,
-Vinay