Getting the codes read is a good place to start, as already mentioned. However, a flashing CEL always indicates an engine misfire on one or more cylinders. Some OBDII systems won't tell you exactly which cylinder is misfiring, but it should still indicate a similar code. Likely a spark plug and/or wire or even a coil could be the culprit.
If you have never had the spark plugs changed, now would probably be a good time....