It seems that the positions of the axis labels are affected by being merged with other graphs during the layer arrangement. (Also, it may be related to the label's "Attached To" properties to LayerFrame/Page/Layer&Scales.) I will ask our developers to look at the issue. So, could you please send your Origin files (before and after merging) to us? (http://www.originlab.com/index.aspx?go=Support&pid=752)