Sometimes, when switching to auto-stretch timebase, the dialog box doesn't pop up, and the audio is shifted as if REAPER assumes that the audio is not yet mapped. This seems to happen if there are no tempo changes over the item:
For example, in this screenshot shows a MIDI item (top) and its render (middle), which is of course tempo mapped. There are no tempo markers above the item (except at the edges). When setting timebase to auto-stretch (bottom), the audio is automatically warped without a dialog box: