I have, at the moment, at least 15 applications spread over 5 desktops. Only a handful show up in the session table. Eg., I have at least 6 terminals open. I've noticed this problem a long time ago, but didn't want to waste time on complaining, because the applications do show up on reboot.
Some tasks do not appear on reboot, such as programs which were launched from inside a terminal (I use mc a lot), but that is understandable, as XFCE cannot see what is running in the terminal.
Did you start your favorite programs directly from the menu, or from a terminal? (the java apps too?)
And did you try 'Save session' in the Session and Startup window? Do you have 'Save session on logout' enabled? And do you actually use the commands to shutdown/logout?
Also, have a look at ~/.cache/sessions, where the actual session is saved, something like xfce4-session-account:0
. In that file is the actual list of what is saved on logout.
EDIT: The settings daemon has to be running:
1727 ? Ssl 0:00 xfsettingsd --display :0.0 --sm-client-id 218ea527f-3075-47a8-b361-874c0272c6be 5216 tty1 S 0:00 xfce4-session-settings 1710 tty1 Sl 0:05 xfce4-session