Just my humble 2c, but it might depend on how close you get - one or two narrowband frequencies may not be enough to identify a warship or sub - whereas noisy freighters are easier to classify farther out.
I don't know if it's a problem with the latest RA (I doubt it). I have RA1.39 and autocrew classifies warships and subs just fine. I have to be quite close to get the 'correct' classification though!
Cheers mate,
Stew