Tried removing the card, scandisk, soft reset and even a hard reset (thank god for sprite backup). Still not showing the folders.
Another funny thing now, I replaced the schemes and voices folders for TomTom on the SD card but now TomTom can only find them if they are in the root directory of the axim. Looks like something else has screwed up where TomTom looks for the folders.
Tried copying all the files to another SD card but the problem is still there.
Looks like a hard reset and reinstall is on the horizon.