I haven't personally ever seen the 0xfeff characters InDesign uses to hold the xml tag markers trigger a recomposition.
When I've seen recompositions that didn't make sense to me, it has often turned out to be a document created in one version of InDesign, and then converted to a newer version. Touching the text in a particular story in any way triggers a recomposition of that story using the current, newer engine. Have you ruled that scenario out—by, for instance, recomposing all stories (command-option-/ on the Mac)? Just an idea.
Jeff