We eventually found the answer to this.
Excel will only respect the escaping of commas and speech marks if the column value is NOT preceded by a space. So generating the file without spaces like this…
Reference,Title,Description
1,"My little title","My description, which may contain ""speech marks"" and commas."
2,"My other little title","My other description, which may also contain ""speech marks"" and commas."
… fixed the problem. Hope this helps someone!