Hi Daniel,
I experienced a similar problem bringing up a RPI2 for a friend; the toolbar 'Mathematica' button stopped working after updating and upgrading an Element 14 Noobs + Recovery micro SD card (SK 40522 71053). Curiously, my own RPI2 SD card, derived from a 'raspian-jesse' image download dated 2015-11-21, worked fine after the update/upgrade.
Inspecting the file "/usr/share/raspi-ui-overrides/applications/wolfram-mathematica.desktop"
from both RPI2's suggested the following fix, which solved the my problem:
Contents NOOBS/RECOVERY "/usr/share/raspi-ui-overrides/applications/wolfram-mathematica.desktop"
[Desktop Entry]
Encoding=UTF-8
Type=Application
Version=1.0
Name=Mathematica
Comment=Technical Computing System
Icon=wolfram-mathematica
TryExec=/opt/Wolfram/WolframEngine/10.0/Executables/Mathematica
Exec=/opt/Wolfram/WolframEngine/10.0/Executables/Mathematica %F
Terminal=False
MimeType=application/mathematica;application/vnd.wolfram.cdf;application/mathem$
Categories=Application;Development;
StartupNotify=true
Change following lines to match the file contents seen after the "raspian-jesse" SD card update/upgrade:
TryExec=Mathematica
Exec=Mathematica %F
The changes were made from a command line terminal using the 'nano' editor:
cd /usr/share/raspi-ui-overrides/applications
sudo nano wolfram-mathematica.desktop
One could also use "sudo startx" at the command line interface prompt to run the GUI with root privileges, then navigate to "wolfram-mathematica.desktop" using the file manager, then make the required changes using the text editor. To revoke root privileges, exit to the CLI and restart the GUI using the regular 'startx' command.
Best Regards,
Layne Wright