Under the Advanced settings it is possible to tweak what MakeMKV is looking for when it rips a disc.
The original string is:
-sel:all,+sel:(favlang|nolang),-sel:mvcvideo,=100:all,-10:favlang
Which basically selects favourite language files and no language files, and deselects mvcvideo (3D) files. No idea what the bit on the end does but it does explain why my 3D films never worked properly.
From looking on the MakeMKV forum I’m now using:
-sel:all,+sel:(favlang|nolang|mvcvideo),=100:all,-10:favlang
which should let me rip 3D films and, now that I’ve sent falling to English, only selects the English tracks.