I recently had a friend ask me if I'd heard about noteheads becoming screwy after updating to Sibelius 6.1. I hadn't actually experienced this, or heard anything from other users about it, but he solved it by contacting Sibelius support who gave him the following explanation. If you run into this problem, hopefully this will help get you back on track.
--- [i]When running Sibelius 6.1 , you may encounter noteheads, clefs and other characters inside Sibelius do not appear correctly: either the wrong symbol may appear, or the symbols may actually be completely invisible. This is caused by a problem with the fonts getting activated that is specific to Mac OS X.
[b]To fix this:[/b]
-Run Font Book from your Applications folder
-Select all of the Inkpen2, Opus, Reprise and Helsinki fonts using Command-click
-Right-click and choose Disable Fonts
-When asked to confirm, click Disable
-Now right-click again and choose Enable Fonts
-Now run Sibelius again, and you will find that the fonts appear correctly once more.[/i]