Not sure where is the place for changing this as default.
If you create a WebService object you can issue:
myObject.TimeOut = time in miliseconds
It's actually
myWSObject.Property("Timeout") = 60 * 3000
My mistake was that I was putting this code in the ASP Script of the Web Service Listener - Instead, it goes in the VFP Code where you instantiate the WS Object.
I found the example on MSDN - I tried looking for it again but had no luck finding it.