You probably have a grounding issue. What kind of scantool did you use? To make sure you might want to have it tested at a ford dealership. The WDS and NGS that they use will display a LOT more codes and PIDs than any generic scanner (even if it's Ford enhanced).
SOme older lincoln are known for flashing the DLC light after EEC testing. The dash simply has poor wiring.
Like you said if there is no probem (other than the obnoxious flashing light and can deal with it) don't worrie about it. Mind you if you go to a dealership to have it fixed they will probably charge you straight time. That can get pricy fast.