I think it's prudent to set up Silk so that the global setting is to have text smoothing disabled. Then, add whatever applications that you want to use Silk for. I've been doing this since the second original release of Silk and have never had any problems.

Frankly, there aren't that many applications that need Silk. In my case, it's Appleworks (Silk is waaayyy better than the built-in smoothing in latest AW release), Dreamweaver and Photoshop Elements 2.0.