First off,Hi and welcome to the board.Its usual for newbies to get a round in at the virtual bar,.......mines a pint of Stella.
You could be worrying about nowt,as the red limit light is supposed to flash when the key is removed from the ignition.Its perfectly normal,its just the ECU telling you the bikes imobiliser security system is working.
The red light does switch itself off after a while to conserve the battery.
You should be able to find all this info in the bikes handbook.If you dont have the book,you can download one from Ducati.com.
There ya go,...all the '04 handbooks here;
http://www.ducati.com/bikes/service/...delName=2 004