we need to know how you got the music notation into the pdf in the first place, else it's all guess work
can you upload a sample + a how you did it .
the obvious fix, which some kindle music books use, is to add the music as images, with no attempted text conversion
FYI
the big web sites who sell sheet music as "pdf", use plugins like Scorch. so what you get is a scorch file not an actual pdf. you can get scorch for ipad from teh app store, to see it in action
http://avid.force.com/pkb/articles/en_US/FAQ/en391291
http://www.avid.com/products/avid-scorch