I know this is an old post but I just installed the new clockworkmod superuser and I am getting the exact same error. Every other app that requests root is working just fine.
I have never been able to get "use root" to work in Tasker. I've given up trying and now use Secure Settings whenever I need a task to use root access. Its just a habit now.
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I had the same problem and went looking for a solution, until it's fixed you can work around it by creating an empty file called:/system/app/Superuser.apk
Tasker should have a more reliable check if su is able to be run as this is the first app I have found with issues with Koush's new superuser app.