John,
I think that the Fioan/Shrek bed scene (that sounds worse than it is) is supposed to sound that way. I think that the band is caleld the Eels and the singer's voice is supposed to soudn that way. I too thought that something might have been wrong in the recording of the soundtrack, but listened to it elsewhere and heard the crackling (like a distorted recording).
About the other two things, I can't comment, except to say that I didn't notice any problems in those scenes when listening/watching. It may be your copy of the disc or your impecable ears.
