Do not confuse "looping segments" with "looping audio clips inside segments". Looping an audio clip inside a segment means that the user has stretched the clip that appears in the Segment Editor (a blue triangle appears - see below). On the other hand, looping a segment is only a degenerated case of scheduling synchronized segments one after the other by the interactive music engine, within a Music Playlist Container. The simplest Playlist, with just one looping segment in it, requires much more than just looping the files underneath. In fact, the interactive music engine has to take pre-entry and post-exit regions into account, dovetailing segments, deal with streaming look-ahead time, starting and stopping one or multiple clips inside one or multiple tracks of each segment instance, at the appropriate time. Thus, when a segment loops, the audio clips inside its track do not loop. It is a whole bunch of new instances of these sounds that get created at each "loop".
Consequently, 2 distinct audio clips in a music segment always end up being 2 distinct sound instances. Likewise, the same audio clip of a looping segment always results in 2 distinct sound instances every time the segment is looped over itself.
Now, audio clips themselves can be stretched inside the Segment Editor. When you do so, a blue triangle appears on the upper edge of the clip. Whenever a blue triangle appears, the sound is played as an infinitely looping sound, and is stopped explicitly by the interactive music engine when the cursor hits the "end position" of the clip. If you don't stretch the clip and there is no blue triangle, the underlying sound is played as a one-shot sound. Thus, stretching a clip has non-trivial consequences over the way sounds are treated at lower levels, especially when it comes to I/O.
About embedded wave looping cues
As we have seen earlier, segment looping occurs at a different logical level than wave looping. Segment looping occurs at boundaries defined by the Entry and Exit Cues, defined for each segment, across all tracks, in the Segment Editor.
In Sounds of the Actor-Mixer hierarchy, looping sounds use the wave looping cues (embedded with an external wave editor) as looping boundaries if they are looping. If no wave looping cues are embedded, looping occurs around the whole file.
Audio clips inside segments obey the same rule if they are looping (that is, those that have a blue triangle): they loop around their embedded wave cues. However, a limitation of the Segment Editor's wave viewer makes it unable to display the actual looping region, because it is unaware of the presence of embedded looping cues inside wave files. Consequently, you will not hear what you see if your stems contain looping regions. You should remove embedded looping regions from files that you use within the interactive music system, or at least, ensure that you avoid stretching their clip so that they become looping.