Utrabeat is starting the sample from the same place (if you bounce it, you can see is is in phase with the original), but it is making a zero crossing at the sample start.
As a test I used the pencil in the sample editor to make the first zero crossing in the sample really far in and bounced it out of Ultrabeat. It's still in phase, but the sample starts at a zero crossing. With a bit of a fade in, even though I had none in the ADSR.
See the attached pic, the waveform on top is the original sample, the lower one is after playing it in Ultrabeat.