There is a chance that the data is being returned and the query is fetching a big result set.
You could check the value of the query timeout in the Virtual DataPort Administration Tool by going to “Tools -> Admin Tool Preferences -> Connection” . This value could have been set to a higher value due to which the query is not timing out. I would recommend to set it back to its default value, which is 900000 milliseconds, so that the querying stops when the timeout is reached.
Hope this helps!