Why are logic board replacements always a source of grief?

Just what is it, anyway, with the times when you have to get a logic board in a computer replaced? Is it only an Apple Macintosh thing? Every single encounter I’ve had with the procedure has resulted in some sort of complication.

Never mind the fact that after mine was done recently, I had to re-authenticate iTunes, re-enter registration codes on some applications, and start over on my Time Machine backups, all because everything thought it was a new computer.

No, what I’m talking about are the things that aren’t supposed to be part of the replacement. On my MacBook Pro, there’s now a faint hum I can hear when I attach external speakers. Volume settings are all still the same, but that hum was not there before my original logic board failed.

Meanwhile, @rickmacmerc has also been experiencing issues after a recent replacement—more serious than just my little audio hum.

Further case in point, a good many years ago, the ethernet failed on a G3 tower at work. Since the ethernet was on the logic board and not a separate card, the whole board had to be replaced. When it came back, it would appear to boot properly, but start suffering random freezes after several minutes.

Is this a common story? Has it happened to you?