Multi-language Rise courses and LMS

Bit of a long shot this one I know, but I wonder if anyone has experienced similar to this...

We have a Rise 360 course that has been translated into 13 languages. The Rise translation roundtrip was all fine and every XLIFF file imported fine. We then made some manual edits to the text based on additional user feedback, and exported the courses for upload to the client LMS. All good so far. 

Now, the client LMS uses some sort of multi-language module to attach different language versions to a base version (in this case English). So they uploaded the original English version of the course first, then append the languages to that. Of the 13 translations, 10 were added without any issue, but three (interestingly the last three we worked on) can't be uploaded to the same course as the LMS thinks these have a 'different course structure' to the original.

For all courses the publishing settings are exactly the same and, outwith the language changes made first by the translator and imported via the XLIFF file and then the manual text edits, the course structure remains exactly the same - i.e. we haven't added anything new or taken anything out.

My long shot question is, has anyone every experienced something similar with Rise courses and multiple languages and found a workaround? I know it's a very specific issue, so in all likelihood perhaps not, but figured I might as well ask!