I am finding that with release 4 of the N800 "firmware" that kismet more or less works correctly. It sometimes hangs the wireless interface when you exit. I find that exiting using capitol-Q is less likely to put the wireless interface in a unuseable state. I have needed to remove the battery and restart the device in order to get the wireless working again on several occasions.

I do have Skype installed on mine as well. I suggest you check you control panel to make sure you haven't set the N800 to auto scan and auto establish connections and also suggest that you enter the command line (there was a post somewhere around here) that adds longer timeout intervals on the display, which also seems to put the wireless into power saving mode and kills kismet.

The "saving data files" issue that I encounter is that if you leave kismet running for a while, you will eventually see this message in the lower status pane and the wireless interface will sometimes stop scanning after displaying one of these messages. My guess is the wireless interface is doing something funny or power management is kicking in for some reason and that the "saving data files" message is coincident but not causally related.