Try this: Use a jumper wire in the diagnostic port connector, between the black wire and the light green with red tracer wire. Jump them and then turn on the system, and the codes will flash out. If there is just a really rapid flashing too fast to count, that's the 'intermission', the marker between the repeated sets of codes, and if that's all you get, then there are no codes in the system.
Maybe if you get a code #, you can figure what's wrong.
I have a 2000 screaming eagle road glide with 44,000 miles on the odometer. The bike is well maintained and stock. The check engine light comes on for ten seconds after the bike is started and the goes out, this happens warm or cold. The bike did this about two months ago and I reset the ECM by removing the 15 amp fuse, and it stopped. I have a new air filter, spark plugs, and it started doing it again today, I again cleared the ECM by removing the fuse and it is not coming on after the bike is started. Has this happened to anyone? Any ideas I do have a service manual but no scanalyzer.