I've just noticed this same issue. I'm reflashing my N800 to try and solve a rapid battery drain problem that only happened when booted to the cloned OS on my 4gb mmc2. I removed the 4gb sd card and reformatted it to one 4gb fat32 partition using gparted on my laptop running Ubuntu Linux. I reflashed the N800 with Diablo, downloaded Install Tools, removed the external sd card and cloned OS to the newly formatted 4gb internal sd card before installing anything on the base OS. When I booted into the newly cloned OS all the programs from the old cloned OS, email accounts with downloaded email, and contacts were there. No browser bookmarks though. I had installed nothing on the newly flashed OS. I did remove the battery before flashing and I haven't put the external sd card back in since I took it out to clone the OS.

I hope the reflash and reclone fixed the battery drain problem I was having in the cloned OS, or I'll have to try the manual method of cloning the OS so that I get a clean install.

Edit #1: None of the programs that are there from my previously cloned OS are showing up in the installed applications list of the Application Manager. They are all listed, and runable!!! (did I just invent a new word - runable?), in the application menu. They are not installed in the base OS.