The cards should disappear from the file manager when there is a USB connection to the PC. So I guess the problem is that they don't reappear when the cable is unplugged. Perhaps this suggests that the problem is at the N800 end, but I don't trust PCs.

Good to learn that 2x4GB cards does work, though I suppose that could be part of the problem as I guess it takes you somewhat outside Nokia's stated spec for the N800.

Things to test might be - only using one card. Disabling virtual memory so the N800 makes no use of the cards at all.