I think 'running in' is exactly as said above. It's more a case of 'running in' your brain and ears. There is no real physical mechanism to attribute perceived change in solid state electronics during running in. (Other than obvious ones such as drift in bias currents in power amplifiers, but that stabilises in minutes, not months, and in op-amps, in microseconds!)
I've had stuff that sounds great one day, and lackluster the next. If you have a read of some of the psychoacoustics papers out there, experts reckon your mood can affect perceived sound quality quite radically, as does alcohol! I must admit, music always sounds fantastic after a few beers...
Fully agree that double blind listening tests are the only way to decide which is nicest, and measurement is the only way to decide which is most accurate. The outcome of those two approaches may not always coincide
- This is why neither hifi manufacturers OR audiophiles like that test! Audiophiles don't like to be proven wrong, manufacturers don't like to have their kit slated without proof by dumb-ass audiophiles.
"Two very small men cutting steps in the roof of the world"