i have zero scientific evidence to back this up- but yes, I agree that amps break in. Maybe I just burned all the dust off the tubes, but my Marshall really warmed up after a few hours of playing at a reasonable volume.
I've noticed it only one time specifically. Probably because I was trying to record a clip outta the box and had a hard time dialing it in. My speaker cab was old and well broken in, so it wasn't that. This was also an amp model I was really familiar with so I had a good idea where to at least start with settings. I let some time pass and the amp sounded much better. Now that same amp rips and sounds awesome.