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When double-clicking on a Java method in a class that is not currently open (say; org.eclipse.equinox.log.Logger#getName()) the file opens in the editor. However, the scrollbar on the right is always scrolled to the top of the file, regardless of where the view ends up being focussed (which invariably isn't on the same page). Any scroll operation with the trackpad causes the scrolling to instantly jump to the top. The same is also true if a class is double-clicked: the text looks like the class definition is highlighted, but the scrollbars remain firmly at the top. When you make the smallest move on the scroll, it jumps to the top of the file. I'm raising it in the IDE because the same effect can also be seen in a text file with bookmarks. Create an emtpy text file, and add a hundred lines of blank text (more than a couple of screens). At the bottom, add a single line. Create a bookmark for this line. Verify that double-clicking on the bookmark (from the bookmarks view) takes you to this line. Now close the editor, and double-click on the bookmark. The scrollbar will jump to the top of the file, and you may or may not find the bookmark in the right place. Double-clicking a second time will cause the bookmark to jump to the right place. This was tested on OSX 10.7 with Eclipse 4.2.0 - let me know if you need more details or you are unable to reproduce from the above.
You probably see bug 375576 for which we added a workaround for SR1. Can you please test the latest RC for SR1: http://download.eclipse.org/eclipse/downloads/drops4/M20120905-2300/
It does look as if it's the same problem. I'll test it out and let you know.
Yes, the fix in the nightly resolves this problem - though I noticed a slight flashing of the window from time to time as new views and/or window was opened. But this bug can be closed as fixed in 4.2.1.
*** This bug has been marked as a duplicate of bug 375576 ***