I have some experience in this field and I believe PEX_RUN variable enables or disables creation of extraction layer translation. So once your LVS completes, if PEX_RUN is set to true, all the CAD layers from your layers are mapped to physical layers that are in the technology file (transistors, vias, metals) for RC extraction. I think that your LVS fails when you turn on PEX_RUN to true because Calibre is not able to map the CAD layers to the correct technology layers. Check and see the technology mapping file to ensure that all the CAD layers are correctly mapped.