Did you load the sound files AND the chain files? Hard to believe the strobe didn't change to the desired rate with all the files loaded from the engine you're trying to match. Also, it's possible that the files shown on the page for your engines don't match what was loaded into them to start. You could also load the sound and chain files into the other engine to match the upgraded one.
If that fails, have you thought if perhaps interposing a little circuitry and creating your own strobe drive? Since there is a signal you can tap off, I can think of a fairly simple method of sensing when the strobe is active and just driving your own strobe generator.
