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If the Problems View is open on a perspective that is not active, it continues to queue background Jobs and updates its state based on the workbench's selection service. This is wasteful processing of selection changes. The User may have views in the foreground that are fighting for background CPU cycles with such views that are not "active". It also impacts battery life. Almost all views either push (and therefore often have a sync-with option), or pull from the selection service. So, this problem is not specific to Marker Views. In my workspace, I have configured the Problems View to show problems of selected element with children. This is probably the worst case scenario as the list is dynamic, but also lengthy.
This is fixed in the new markers view.
Verified in I20080205-0010