Bug 127289 [Markers] SystemFilter and group selection state not preserved
We are not preserving the selection state of the system filters or which group is selected.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/views/markers/internal/MarkerFilter.java
while (parentResource != null) {
					if (parentResource.equals(focusResource[i])) {
						return true;
					}
					parentResource = parentResource.getParent();
				}
			}
		}
		return false;
	}
	/**
	 * Returns if the given resource is enclosed by a working set element.
	 * Previous versions of this method used IContainmentAdapter for containment
	 * tests. For performance reasons, this is no longer possible. Code that
	 * relies on this behavior should be updated appropriately.
	 * 
	 * @param element
	 *            resource to test for enclosure by a working set element
	 * @return true if element is enclosed by a working set element and false
	 *         otherwise.
	 */
	private boolean isEnclosed(IResource element) {
		if (workingSet == null) {
			return false;
		}
		if (workingSet.isEmpty()) {
			return true; 
		}
		Set workingSetPaths = getWorkingSetAsSetOfPaths();
		return workingSetPaths.contains(element.getFullPath().toString());