Yeah, it is pretty annoying, but like so many things I’ve just gotten used to it! 🙂
I’ve run into this type of problem because I’m doing my main compositing work in Shake but all my main roto work in Silhouette Roto. I had bought the FCP/AE plugin version of Silhouette previously and at the time had thought it was a pretty neat idea, but have lived to regret it since I’m working with image sequences in Shake projects, so I then have to convert ’em to self-contained QT movs to bring into FCP, place the Silhouette Roto filter on ’em, etc.; a really cumbersome way of working (although I’d have to export the shapes back into Shake anyway). And because of the non-linear editor drop-frame etc. nature of FCP, a lot of times I will have to deal with missing a final frame in which I have to tweak the roto shapes directly in Shake’s cumbersome bezier rotoshapes which was what I was trying to avoid in the first place!
But for me the better solution will be to upgrade to the most recent standalone version of Silhouette so I can just work with image sequences natively. (Otherwise, handles are the way to go.)