Quote:
Sometimes tracks seem to have had several minuites of silence tacked onto the end!

This might just be the tracks themselves. Some albums have CD-ROM data tracks at the end, which, depending on your ripper software, get turned into long silent gaps at the end of the last track of the album. Also, sometimes "bonus tracks" on albums get ripped as lastsong+silence+bonussong. Check your original source MP3s on the PC to see if that's what's happening in those cases.

For your other problems, definitely read the FAQ entry that TMan linked above for the explanation and repair information.
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Tony Fabris