He didn't have a hunch, he just knew that the standard comprehensive test was skipped, which is why the standard test procedure only detected a problem, and he had to end early and go off book in order to reveal the doppler problem.
> Fortunately, Claudio Sollazzo, Huygens's ground operations manager at ESA's European Space Operation Centre (ESOC) in Darmstadt, Germany, had a nagging worry about the lack of a full-up communications systems test. Sollazzo knew there was time to run some tests during Cassini's long, uneventful stretches between the planets.