Have you gone into device manager and set up one of the posts to "COM1/2/3/4"? You need to do this!
I have the ebay shareware version of VAGCOM and have noticed that on my car (2001 AUM 1.8T) it will only read fault codes etc with the IGNITION OFF, if i have the ignition on it simply stops responding. BUT when i scanned a chap on heres TDi for him, it would only work with ignition ON. I'm assuming this has something to do with the older versions of vagcom and the different types of clocks?