Hi Geoff,
If you set BeatsPerHyperBar to a very large number (like 1024 or larger), then when you set the controls (!MaintainPitch, !MaintainTimeToNext, !MaintainPosition) to their max values of 1, it will play through the sequence in the original order.
Am guessing that the files you are using have a cc07 message hiding somewhere; if you still don't find it, though could you send a short example exhibiting this behavior to us by email?
Thanks!