trouble with tracks(and sometimes sequences) overlapping?

I have yet another seemingly impossible question again. I will make several tracks trk 1(bass) trk 2(chh) trk 3(kick)trk 4 (snare) and trak 5(main sample) and trk 6(secondary sample for verse 2)-well when im in trk mute mode and i manually mute trk 5 and manually in trk 6 to take over,part of trk 5 that i had already trimmed off will play(meaning the rest of the sample on trk 5 finishes as if i never trimmed it?and interferes with trk 6 -so basically when i switch trk 5 off and trk 6 on they both play in loop 5 & 6 but 5 will stop after the full sample is done and 6 just keeps on going in loop mode....sorry if this is a bit jumbled but im kinda in a hurry and my kid brother beat me at rc pro am again,little bastard if i could learn how to fix this i would really show him! PLEAE HELP mpc MASTERS