Jonathan,
 
Could you send me your scripts?  I'm trying to do the same thing.  What happens if you copy DLLs and files overtop a running system? (I know what the answer should be, it just keeps running with your new code). Do you have to stop and restart the IIS service?  How do you do this from a build machine? (not the same as the test or production machine). 
 
TPM 

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