Eclipse doesn't save preferences until it quits — gracefully. Now, if it should ever happen that Eclipse (heaven forbid!) crashes or has to be killed, recent preference changes are lost. Keep in mind that setting up syntax highlighting the way you want it can easily take a half-hour given Eclipse's perverse preferences dialog (but that's a story for another day …).
This isn't the only way Eclipse goes out of sync when it crashes. Lord knows Eclipse is damn lazy about refreshing filesystem data (though if auto refresh is on, it's raving-lunatic zealous about it instead). But for God's sake, people can spend a long time tweaking preferences, even when the dialog isn't an affront to all that is holy. Sync preference changes to disk immediately if not PDQ. If the program has to sit for a few seconds when you hit OK so it can save the preferences, oh well. This is Eclipse. Why care about being sluggish only now?
Once you've made your way through the labyrinth that is the preferences dialog (don't be fooled by the search field … if only the dialog were merely poorly organized … but again, another day), go to File → Switch Workspace … and switch to the workspace you're already using. It'll exit and relaunch immediately. Yes, that can take a good half-minute, but at least it's not a half-hour.
Related bug reports
- Bug #149629 is this issue, except I disagree with the solution (the preferences should simply be saved when they're changed).