there are many possible causes for your problem...
here is what you should do to verify...
try burning a CD MP3 that contains the same music where you experience missing sounds... then check if it will recur to what you have described..
if it has possible that you have a problem on either left or right channel of your system... try controlling the balance from left to right and check if they have equal sound output...
if it has not recur possible cause of the problem is the jack you are using.. use another jack and compare... also check your player sound output via earphone and check if the sound you are referring as missing will be heard..