Yes, it has happened to me with a Transcend 4GB card (internal slot) running 1.2007.44-4 on N800 (ie. OS 2008 for N810). The internal memory card is accessible, swap is in use and according to df it's mounted correctly but File Manager refuses to acknowledge I have an internal card, and only lists the external card. I haven't bothered to investigate it much further as I very rarely use File Manager (mostly using ssh etc.)