If you are referring to the 32-mile Leander to downtown Austin line, then the answer to your question is it will be operational in 2008.
If you mean the Georgetown to San Antonio line, then I really have no clue. I believe it will not be done until Union Pacific moves off those tracks. There are negotiations taking place to build new tracks east near the new TX 130 turnpike that would not have any at grade crossings of roadways, and be in a much less populated area, therefore allowing much, much faster speeds for the freight trains.
The voters of Texas approved the creation of the Texas Railroad Reloction and Improvement Fund last year, and hopefully this will help to speed these new tracks construction up, and we can have the current tracks for commuter rail soon.