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I'd agree with the "letting problems surface" shake-down. We still see it even with semiconductors today. Generally, if it's going to fail, it will do so within the first 24 hours of use.
Other than that I can't think of any sort of physical manifestation or effects related to a break-in period like you have for mechanical things (e.g. motor bearings or belt drives getting used to their particular quirks and wearing in to be "comfortable") except for maybe electrolytic capacitors "forming up" as they get used to their operating conditions, which may differ somewhat from the conditions under which they form the oxide layer in the factory.
Then again, electrolytics in bias circuits could very well alter sound slightly if they develop small amounts of leakage as they are worn in... someone more familiar with amplifier theory would be better able to comment on that, I think.
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