It does on my machine running an updated 3.8.49 so .... it might be something else, like you wanting to add applications that don't have a sepcific .desktop file in '/usr/share/applications/'
There's a tutorial on customizing E16 here:
Which might have some pointers you need.
That's 'conky'. It gets started every time you open a new session. Simply kill it with "killall -HUP conky" and if you never want it to start: Either remove oit completely with "apr conky" or ....
Just comment out (with #) the line in '.e16/startup-applicattions.list'
Of course you can also see/check-out if E27 is to your liking.
Where again there's a tutorial:
