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3.6M3 but I think I remember have seen this issue before. I want to compare the current edition with previous local history but because the file is quite big, I use the Compare with -> Element from previous History... on the method instead of the entire java file. Then the History view opens with the local version of the method and selecting one in the list makes the Compare editor opening, as expected... But the compare editor content is totally unusable! It seems that on the left side, the entire compilation unit is displayed although only the method is displayed on the right side, hence make the comparison regions difficult to be synchronized... Note that I didn't get the same issue while using Replace with instead... The compare editor contents is correct when using this action.
This sounds like a dupe of bug 291695. *** This bug has been marked as a duplicate of bug 291695 ***