while in the song mode screen, right after u hit convert, the mpc will ask u which sequence you would like to save the song in. right underneath that, there is an option which can be changed with the toggle wheel. highlight that option and scroll until it says "off tracks ignored"
i often have that same problem and scrolling thru the options in the song mode until "off tracks ignored" is selected should be the answer. i hope u can unerstand what i wrote.
hope this helps.
out.