I've noted this myself, actually. As an anecdotal example: when I was younger I was lucky enough to get an antique German violin, heavily discounted due to damage, but it looked a lot worse than it was and my teacher knew someone who could restore it. After restoration, it was gorgeous, but it still sounded "stiff", for lack of a better word - no depth to the sound, not letting me get much subtletly out of it in terms of variation in volume. After a few months, though, I could hear a difference, and after a couple of years it was amazing. Some of that will be my skill improving, but that can't account for the timbre of the sound - rich, resonant, beautiful. My teacher commented on it, and said it was normal for violins to have this period of "settling in" - most notably in new violins, but also in older ones that have experienced a change - like this one, that had been re-lacquered, amongst other things. (She used to be lead violinist for the city symphony orchestra, so I tended to take her word on all things violin.) Since then I've also noted that a violin tends to sound a touch worse with a full set of brand new strings.
I'm not sure on the cause, but between my observations, my teacher's comments, and some educated guesses, I can point to a few factors.
My violin was already an antique, so it's unlikely to be anything solely relating to age, although that may play a part. My theory (which is mostly guesswork) is that it's to do with anything that's absorbing, damping, or altering the vibrations in the violin.
- Fresh strings aren't used to being under tension, so they need to stretch in a bit - which is why you have to re-tune more often for the first week or two (or so it seems to me).
- Various parts of the violin aren't solidly fixed, but are simply held in place by tension or friction - the bridge and pegs, for example. The bridge in particular plays a very important part in transmitting vibrations to the body of the violin; I know from experience that even a hairline crack in the bridge can have a noticeable effect on the sound. I reckon that with new strings (or on a new violin) the bridge is still moving very slightly as the violin vibrates until it settles into a stable position.
- The body of a violin flexes subtly; you'll notice that variations in temperature and humidity can affect the sound (I remember having to re-tune midway through a concert because my violin had gone from a cold car to a hot concert hall too quickly). The tension of the strings is likely to cause an imperceptible flex in the violin, and this will change as the strings stretch in and the various parts settle.
- Fresh strings don't have that slight coating of rosin in front of the bridge yet, so the bow doesn't grip them in quite the same way. In general, the better the grip, the clearer the tone - clean horsehair sliding on clean strings produces a sort of hiss, so if your strings are new you'll get this slight interference in the tone.
- This is a bit of a stretch, but anything that vibrates may have a degree of inelasticity. In terms of the physics, that means that as the violin vibrates, some of the energy is converted to sound, but some is absorbed by the material of the violin to produce small physical changes. (This is true of anything that vibrates or flexes; it's why suspension springs give out eventually, for example - gradual metal fatigue due to repeated compression.) In a violin, it's possible that it causes subtle changes in the wood and/or lacquer (and the adhesion between them). This may cause a change in the character of the sound.