I have noticed that the amp is now, after 3 months or so, a lot brighter than it was and I now have the presence and treble controls near noon whereas previously they were much higher , especially the Presence. The clean tone is a lot more articulate and chirpy.

Since there are a new batch of OTS amps out there and many people are reporting they can't get the same tones they have been hearing in the online clips I'm wondering if the amps do need a period of break in. If that is the case what components need that break in period? Valves? caps? seems unlikely to me, but its definitely the case here that the amp has improved.

I am a newbie in the guitar amp world, but have more than 25 years experience with high end playback systems. Nearly every component needs to break in. This is easy to understand with speakers, where at time lengthy break-in periods (many weeks) are even explicitly mentioned by the manufacturer and less explicable with cables. It goes without saying that warming up of a component (amp) is mandatory in order to reach its full potential. My stereo (solid-state) amp needs approximately 2 hours before it is on its hights of reproduction. I don't see why this all should not as well apply to the guitar amp world. I do not know also why it is like this but feel that this lack of explanation does not matter. Explicable or not - let your ears decide.

Absolutely. But letting aside any psychoacoustic (the ears that do need a "break-in" resp. get accustomed) and philosophical staff (of what nature is it what you call sound anyway - and therfore is influenced by what ?  , on a conventional level speaker membranes are changing consistence and behaviour while being used, components change their characteristics etc. And here is one more: My amp (of the stereo that is) does play best on sundays. That seems quite -- to put it politely -- "extravagant" at a first glance, but apart from the aspect of assumed greater relaxation of the listener itself there is generally less "dirt" on the power line. This difference is there and definitely audible, believe it or not. It comes to my mind how everybody talks about a "tone quest" in the area of guitar amps while easily accepting noises from effect pedals, humming, buzzing and you name it. Is this part of the "tone character" that so many seem to be chasing ? 

Somewhere in the Forum-someone suggested leaving it on for a few days. Does it matter if it is on standby?  And does this burn in the tubes or the amp itself?

With Volume at 4 and Master at 5 and all preamp switches up and with a Sadowsky Semi-Hollow both pickups selected and tone control up (all on clean channel, no OD, no boost) I get quite loud but it wont knock me off the feet (I may play like this at home - although not very long I suppose ;-) -> neighbor alarm. Forgot to mention: I currently use a Mesa Thiele closed back cabinet with a 12" C90. Is this what you refer to as loud or did you mean with OD and boost ? I am asking because I  look for a reference on loudness for my OTS. Just wondering, maybe you can tell me what you think. and by the way..mine is just on the way to break in as well.