I have no way to reproduce this...
I recorded a sample on an audio track. It seemed fine, the whole sound was playing back. It was two big orchestral hits. Then I went into the audio recording to edit the sample, moved the start point to the first orchestral hit. Then I went back to song, chopped the audio sample off at the start of the orchestral hit, and moved it where I wanted on the timeline.
Then I split the clip to get a the second orchestral hit, went in to edit that sample, got the start point where I wanted, back to song, move it on the timeline.
I repeated each of the samples and placed them additional places on the timeline.
Composed more... then I noticed the samples were only palying back the first second or half a second, not the entire sample tail which went on at least 3 bars.
So I saved my project, restarted beatmaker3, then I got an error message that BM3 couldn't find a sample that was used in the project.
Searched the entire bm3 directory, no luck, my orchestral samples are gone =\