Hi Beggar
I belive this function and problem came with Protool vers. 5.0. At that time I ran into the same problem as you did now, so I contacted our Siemens supplyer, and they told me this trick. Today I Repair all scanlogerrors after finishing a project.
When you are in the Cross reference, you press Ctrl and right click the mouse. Select Scan all logerror. Press Ctrl and right click the mouse again, and then select Repair All.