Hmm. If you ARE using beta 5 (which partly fixed this problem), it may be that this is a bug with the Cocoa text system rather than Scrivener specifically. Certainly, earlier betas made the problem worse, but I think I fixed it (mostly) for beta 5. However, you can see this problem in Nisus Writer and other Cocoa apps in some situations, which makes me think that the problem may lie deeper than Scrivener’s implementation.
That said, what scale text are you using? (In earlier betas, the problem affected non-100% text.) And are you definitely using beta 5?