When you have mobi problems like this it's usually best to suspect the Mobi format/Amazon is at fault, because they usually are:
http://www.knowing.net/index.php/200...-improvements/
http://forums.kindledirectpublishing...essageID=10385
Looks like if you put your chords in <pre> or <code> tags they might look ok on the Kindle. I'd suggest asking in the Kindle/Mobi sub-forums for more detail.