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When navigating to a file, say via JDT "Open Declaration" and that file was not open, the file is scrolled into the correct position to view the area. When (on a mac) using two finger scroll to scroll slightly above the currently displayed area, the view is scrolled to the top. This started with Juno. If the same navigation is done again (now with the file open/in a tab) it works as expected. This is very irritating and breaks the flow of thought; "where was I"? Where am I now? Marking this as a major issue - I am about to go back to Indigo. I have not tested if this happens in other editors that the Java Editor, I hope I reported the issue in the right place.
I suspect you see bug 375576 for which we added a workaround recently. Please try with either latest I- or M-build: 3.8.1: http://download.eclipse.org/eclipse/downloads/drops/M20120829-1000/ 4.2.1: http://download.eclipse.org/eclipse/downloads/drops4/M20120829-1200/ 4.3: http://download.eclipse.org/eclipse/downloads/drops4/I20120828-0800/ *** This bug has been marked as a duplicate of bug 375576 ***