This is a known issue in ispLEVER version 8.2 of the software, as the bitstream generated using this software is
not supporting True LVDS output on the left and right sides of the device. Refer to DS1021, LatticeECP3 Family Data Sheet.
http://www.latticesemi.com/view_document?document_id=31998
As the ispLEVER software has been discontinued, Lattice recommends to migrate your designs to Lattice Diamond Software.
http://www.latticesemi.com/Products/DesignSoftwareAndIP/FPGAandLDS/LatticeDiamond.aspx