Well, it seems fairly obvious to me that something is wrong with your install of the pro upgrade, because nothing has changed. Your problem, is that you're using the free version which allows only 30 seconds of output. Check your install. How, I don't remember because I haven't had to use .wmv in 3 years. Maybe you should check on using flash or h264. Something a little more friendly.
To check if the Pro version of Flip4mac has been installed, see if you have any 2pass options on your presets. If you only have 1pass presets, it has not installed correctly. This happened to me when I first installed it. Mutilple re-installs didn't work so I made a quick call to their support and I was off to the races.