And I said No to both Q's so expected that it would then go away and not ask me anything... but then it asked about MC2... so thought maybe it was a way to save to MC2.
I only have one MC, and it still let me transfer money from my GT3 save OK. It seems that you can only transfer licences from GT4: Prologue though, at least in the PAL version.
Go to your home in GT4, and in the top right of the screen click on status. One of the options should be to transfer data or something to that effect. (I think you have to press start) The game will then check both MC slots looking for GT3 or Prologue saves. If it finds one, it'll offer you the option of transferring up to 100,000 credits from your GT3 save, or the first two licences from Prologue.