I couldn't figure out a way to describe this bug I came across without being completely confusing, so I just recorded it instead:
http://www.youtube.com/watch?v=qMEQtVH7JNI
Basically, when I install Scriptographer (Mac OS 10.6.5, Illustrator CS5), and start working on a 2nd document or tab, I can no longer select any of the Illustrator text or numeric entry fields (such as stroke size or opacity %.)