Which tool are you using for LVS? There are a number of different Cadence LVS tools (Dracula, Diva, Assura, PVS - possibly some other more esoteric choices), plus several from other EDA companies (e.g. Calibre, Hercules).
Note that your second paragraph doesn't make sense - there wouldn't be a setting in "spectre" (which is a circuit simulator) which affects LVS (a separate tool).
Also, which version of the IC tools are you using? (Help->About in the CIW).