That makes at LEAST two of us. AFAIK, there is nothing 'special' about the format of the SD card on an NB1 system, and I think you've long since proved that by using your existing card any number of times in a reader slot on your Mac, and manipulating it using Home.
IF - AND ONLY IF - I honestly had a clue about how TomTom is managing this particular model, I'd consider copying the whole thing off to your Mac with Finder, formatting, and copying it all back. But without knowing EXACTLY what they've done that might for some reason be different, I just can't recommend that.
I'm hoping that someone else with one of these units will pop up so that we can take a look at how the card looks and behaves on a PC when it's acting normally. From that, we could decide on the appropriateness of a reformat job.
Have you ever previously used the Mac or Home to perform a full backup of your card?