If you set the value of a pin via the plugininterface, and the pin information didnt exist in the patch xml, that value is not being saved.
E.g: The Tag pin of an IOBox is not automatically filled and created in the patch XML when you create that node. Now if you set the Tag pin value via the Plugininterface, for example the Pinserver (not via SetPatch), the value is set correctly. It even shows up in the patch xml you get through getPatch. But when you save that patch, the information is lost. You have to create the field first either manually or via setPatch to be able to save the data that is held in there.