Whenever I compiled a project in Project Builder shortly after upgrading to 10.2.8, I kept getting warnings about not being able to use a number of precompiled headers due to a modified header file. Not only did the warnings annoy me, but they greatly slowed down compilation time. To rebuild the precompiled headers, open a Terminal window and type:
% sudo fixPrecomps
Now I don't see those warnings anymore, and my compiles are nice and quick.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20031022133818732