Reports are filling the blog world that allegedly there is a “Black Screen of Death,” occurring on the 3DS where the system has to be rebooted to get over the issue. I don’t own one of these, but in case anyone has hit it, here’s some links, That might be of use.
Nothing is on the Nintendo site regarding this issue, so it may not be correct and it could be user error but if your looking to update your system, Nintendo gives the following link.