OK this got me so irritated that I found a work-around. It took me since beta 3, but it works.
I tried all sorts of things but this will work.
Don't set numberOfLoops at all, OR set numberOfLoops = 1; // means loop once
Now make a variable (i.e. myVariableToKeepTrackOfAddedCopies) that keeps track of the number of times you will actually perform the following:
In your MIDIReadProc at some point BEFORE the track has finished playing, do the following:
// Copy the track to itself - effectively doubling the length
MusicTrack theTrack=nil;
MusicTrackGetProperty(theTrack, kSequenceTrackProperty_TrackLength, &trackLen, &trackLenLen);
trackLen = 4.0; //<-- this is your real track length
MusicTrackCopyInsert(theTrack, 0, trackLen, theTrack, 0);
myVariableToKeepTrackOfAddedCopies++;
So now your track is twice as long before it ends and the track will continue. This will work the same as looping except you are taking up more memory since you are making the track length longer after each iteration.
When you stop the sequence/track, cut the track back to the original size.
MusicTrackCut(theTrack, 4.0, 4.0 + (4.0*myVariableToKeepTrackOfAddedCopies));
MusicTrackGetProperty(theTrack, kSequenceTrackProperty_TrackLength, &trackLen, &trackLenLen);
Irritating, but it works. I just verified on iOS9 beta 5. Hope it helps.