I have seen this happening to me few times. In my case I do not connect N800 to PC but when I was trying to remove the internal card.

One workaround is simply shutdown and restart N800. The card should become "free" after restart, after the metalayer crawl has finished its scan thing... (If you have a lot of media files on the card, this may take a while.)

Second option, I just discovered recently, happened when I tried to remove the internal memory card: N800 said the card is in use and offered option (button) to shutdown programs using the card. I closed the battery cover again and clicked that button. After that I opened the battery cover again and it no longer complained about "memory card in use"...