QGIS » QGIS Application

When you have a missing layer when opening a qgs project file, you have the option to find the missing reference file with a dialog. When you choose the correct reference file, instead of keeping the layer/reference file in the same relative position within your layers or "map legend", the layer is promoted to the topmost position. This affects the map canvas by changing the order of your layers. The ideal behavior would be to keep the layer in the same relative position amongst the layers in the map canvas as it is in the qgs project file when opened. I assume this behavior is the same across platforms, but I've only tested on OS X.