Greetings all,
I've just done the apt-get update apt-get dist-upgrade after adding pi-package to my Jessie, and I too have the problem of the missing "add remove software" option in the Preferences menu.
I have indeed run the Main Menu Editor and the option is ticked there. Rebooting has no effect.
I have 9 options ticked under Preferences, only 5 appear on the menu. The missing ones are:
* Add/remove software
* Package Sources
* LxKeymap
* Display Settings.
Moving other stuff up and down (exceedingly slow on a 1 core Pi B) or ticking and unticking etc, has zero effect.
EDIT: OK, suddenly, and for no reason I can fathom, Lxkeymap has appeared on the preferences menu. However, it's in the "wrong" place as per the order that I have defined/requested in the menu editor. The rest are still AWOL. Who knows what tomorrow brings!
Cheers,
Norm.