[this is on cubase 6.0.7 x86 running on PC w7 x64]
the issue can simply be demonstrated by importing any audio file (into an empty project), let’s say the audio is not in musical mode and is set to elastique - time. when opened in the sample editor’s free warp tab and moved around a bit, i place my project cursor on the timeline while zoomed-in to sample-precision so i can see where exactly a transient emerges from the zero-crossings within that manipulated audio event’s waveform in the arrange. i then either flatten the track from the sample editor inspector’s ‘process’ tab, or ‘bounce’ it: in either case, that zero crossings of that manipulated sample always moves away from where the cursor had been placed. ie. the audio after bouncing / flattening shifts. at least its waveform display does, because it could simply be just a redraw issue…
(makes me think the only way to properly record a warped event in the state it’s playing before being flattened is to realtime-record it in another channel – not very convenient.)
(also, on a related note: i’m not sure why, but while keeping other settings intact and leaving a sample in say elastique - time mode, i sometimes get the option of selecting the flattening algorithm in the ‘process’ tab of the sample editor; other times, the only option to choose from is “realtime”.)