Probably the single greatest gripe people have with Eclipse. It doesn't auto-sync with external processes. Probably to keep it OS-netutral.
F5 works on the
Java Perspective, but some of the other perspectives don't have the Refresh menu option bound to F5.
You also can get the "Out of Sync" complaint if you run
Ant and it modifies files then attempt to do a CVS update or Export of your project or something like that.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.