I think this is a sampling problem and not an octatrack problem… zero crossing sometimes is just the best crossing, and not necessarily zero… If you wanted, you should go with the shortening of the samples, and try that LFO trick…
And I think having a pad, or a bed of white noise… or a drone on the tonic of the song your in… or room tone… all of these are a great way to smooth over some irregularities… and it doesnt have to be loud… you can have it faint, and it will still do the job.