Can I get coverage data for manual / GUI automated testing?

I need to be able to get code coverage data during automated regression testing (SilkTest). We test against a release build that is installed. i.e I'm not running unit tests or running from within Visual Studio.

I have tried to run dotcover from the console using the analyse command. I pass my executable, working dir, temp dir, and out put file name via an xml file. On the console I can see that a coverage session has started, and then finished. I can also see that some files are being written to my temp dir. However, when I close my app all the files are simply deleted, no output xml file is created and the console reports "No snapshots were created during coverage session".

Am I doing something wrong? Is this simply an unsupported usage of the tool?

Thanks.