Then I would guess that it was how they are formatted. Technology tends to change and sometimes it leaves some things behind in the dark ages. So even the same program when it is updated can change and not work the same, this is a guess, not for sure.
Are you writing to the cards the same way? I have a brother and not Janome but a lot of them a similar. when I upgraded programs to the 7 I have to write to the cards for the older one a different way and can only put one design on a card for the machine to read it, otherwise I get an error message.