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Background: we had this old homegrown logging system that I'm replacing with Log4J. I marked the old class (Logger) as deprecated, and all the occurences showed up in the Problems view. Now when I replaced all occurences of Logger.error() with log.error(), and adding a static instance of Logger (the Log4J type this time) named 'log', the problems do not show up anymore in the right margin, but they're still in the left margin and in the Problems view. I've made lots of similar changes in the past and never saw anything like that. Fixing other errors correctly removes them from the Problems view. I'm guessing it might have to do with the fact that the old deprecated class and its replacement both happen to be named "Logger".
You need to build the project for these errors to disapear. You must have turned off autobuild accidentaly. See Window > Preferences > Workbench > Build automaticaly.