This may be old news to some of you. A known challlege with FCS2 stabilzation is that it must analyze the entire clip (even if in background). Well, if you have 10 seconds from a 10 minute take, that is a real issue and will take a very long time.
A quick workaround is to send to Motion and do the stabilization there. Motion only analyzes the in/out point range selected...much faster! It also automatically updates your file in Final Cut so not need to manually do it.
I am finding this incredibly useful. 
Yes, this round-trip can solve the time issue. However, there is another method to handle it within FCP. It is a question of taste, but you can use subclips during editing, instead of using only the master clip and making in-out points and drag the selected video to the timeline. I used to select the in-out points as well, but after this I make subclips - small clips from the big clip. At the end, I can even delete the original clip, since I have selected all those clips which are needed to the project. Or, if you have enough space, you can keep it, since you can make from any subclip another one. A subclip is independent from its origin.
The reason behind subclips is: you have to work with smaller clips. And, in case of the Smoothcam filter, it will analyze only the selected subclips and nothing more. If you like to make round-trips to Motion and back, it is OK, it gives the same result, I wanted to show only another way...
Jules