You are correct: saving an mlc in V2.2.3 does produce a Version 2 mlc file, so my Version 1 mlc file must pre-date that! So a workaround would be to re-save the failing mlc files in V2.2.3, which will ‘convert’ them to Version 2 mlc files.
BUT … V2.2.3 will load a V1 mlc file and V3.x won’t (if you try, you get a completely empty Cartwall).
In the files below, test compo clip is the V1 file and test compo clip 2 is the same file, but with a few carts removed, then re-saved in V2.2.3. Obviously, the difference is the extra ‘layer’ in the XML.