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This is related to enhancement PR #2066, were the tasks view is brought to front whenever markers of error or warning severity get added. The tasks view has a feature were you can filter out what type of tasks appear in that view. For the sake of a test case, say that you set a filter to not show Java Problems. The next time a compiling error happens, the Tasks view will be brought to the front, even though there are no new tasks to view (Because they are been filter out.) The correct behaviour would be for the tasks view to only be brought to front, if there were new visible tasks to view. This is particular a large issue, when one has developed a new type of problem markers to be displayed in a different view. The tasks view will continue to grab the focus away, even though there is nothing to view there.
This is definitely a usability problem, however we are in our final fix pass for 2.1 and this is not critical enough to make the cut. We will address this for 2.2. The workaround is to disable the bring-to-front behaviour using the preference on the Workbench preference page.
bug 42967 is similar
the problems view no longer opens or comes to the front for free. There is support (via the view font) to indicate a changed state in the view.