There was a bug fixed a few weeks ago where verse numbers were clashing with chapter numbers. It might be something to do with that bugfix going wrong, but I cannot reproduce what you're reporting in my test case(s).
Could you (a) ensure that you have a recent copy of PTXprint, as updates happen roughly weekly and (b) post a screenshot, which preferably includes a normal paragraph indentation as well, for comparison? (c) also post the relevant fraction of the "final SFM" - see "view" tab in the full view. It may be that changes (either automatic or manual) are changing your \m to something else.
