This has started happening to me now. And from this thread, there are many others who have the same issue: http://getsatisfaction.com/kobo/topi...ice_in_one_day
I have had my KT for over a month without the error showing up. Now it shows up every time I power on. I am on Firmware version 1.9.9 I've been careful about ejecting properly and although I use multiple apps (ADE, calibre) I am careful not to have them open at the same time. Like others I can press cancel when the message appears and continue reading - but I have no idea what it going on in the background and how long I'll be able to continue to ignore it.
Disappointing that this appears to have been around for over a month, yet kobo have not addressed it via one of the firmware upgrades that have come out in that time.