It's quite simple, just do the following.
Open a terminal and type:
gksu gedit /etc/linuxmint/adjustments/10-mintsystem-synaptic.overwrite
Change the line:
/usr/lib/linuxmint/mintSystem/adjustments/synaptic.glade /usr/share/synaptic/glade/window_main.glade
to:
#/usr/lib/linuxmint/mintSystem/adjustments/synaptic.glade /usr/share/synaptic/glade/window_main.glade
Save the file and exit.
Now go into synaptic, and find the package synaptic. Right-click on it and choose re-install, apply the change and after finished exit synaptic.
Launch again synaptic and the missing "Mark All Upgrades" will be back.
Hope this will help.







