Hi Phil,
When you hit Print again, does the chapter number slot into the right position? It should do.
In recent versions of PTXprint we turned on “Quick Run” by default which does a faster, but rougher, job at laying everything out, and only on subsequent runs do things slot into the right place. So hitting “Print” again should solve it eventually.
If you never want to see this happen, and don’t mind waiting an extra 30 seconds or so between “Print” runs, then uncheck that option at the bottom right of the screen:
If this doesn’t solve the issue, then there is likely to be some other marker issue. (Send in an archive, and I’ll take a look).