There are two apps that when I try to open them from the menu they do not open, yet when I run them from the command line from the terminal (using the exact same command as configured in the menu) they run without any errors. Those apps are bleachbit and 4kstogram. I am using the Mate Advanced Menu. Can anyone help me fix this issue?
I’m using 17.10 and it’s fully up-to-date.
Open a terminal (Ctrl + Alt + t) and paste the following command and reset the panel to see if that helps, you will have to add the advanced menu again though!:
mate-panel --reset
Let us know if it helps. 
Nope, it didn’t help. The regular bleachbit entry works, but the bleachbit as root entry doesn’t. Those menu items that didn’t work in the Advanced Mate Menu work in the Brisk menu.
Try changing your software sources download location and updating again which may/may not help?.
You can also try running the following terminal command (Ctrl + Alt + t) in case there are any missing dependencies:
sudo apt-get update && sudo apt-get dist-upgrade -f
Let us know if that helps.
Switching to Brisk Menu fixed the problem.
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Brisk menu is the new default menu in 18.04 if you are interested at all.