I believe the owner's manual says that if the CEL is flashing, it indicates a misfire; one or more spark plugs has been detected as not firing properly. How many miles to you have on your plugs? It could be bad plugs, wires, or coil. The CEL light is yellow; it doesn't change color.

-Mark- '99 Mystique LS, totally original (including the original water pump and the premium stereo)! Bought new in December 1998 for $21,000. 208,000 miles