The error "System program problem detected" comes up when a certain application crashes. Ubuntu has a program called Apport that is responsible for detecting such crashes and upon user consent, report these crashes to developers. This process intends to get the problem fixed by the developers.
However it can be very annoying to common users, and there is no point in showing errors to users when they cannot do anything about it themselves. So you might want to disable them.
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Remove crash report files
The apport system creates crash report files in the /var/crash directory. These crash report files cause the error message to appear everytime Ubuntu boots.
$ cd /var/crash
$ ls
_opt_google_chrome_chrome.1000.crash
_usr_lib_chromium-browser_chromium-browser.1000.crash
_usr_sbin_ulatencyd.0.crash
_usr_share_apport_apport-gtk.1000.crash
Just remove the crash report files
$ sudo rm /var/crash/*
After removing all the crash report files, the error message should stop popping up. However if a new crash takes place then it would appear again in future.
Turn off apport
After removing the old crash reports, if you still get the same error message, then you can completely turn off apport to get rid. Edit the configuration file at /etc/default/apport.
$ gksudo gedit /etc/default/apport
The file would contain something like this
# set this to 0 to disable apport, or to 1 to enable it
# you can temporarily override this with
# sudo service apport start force_start=1
enabled=1
Just set the value of enabled to 0, and this will disable apport.
enabled=0
Save the file and close it. From the next boot onwards, there should be no error messages ever. If you do not want to restart the system then restart apport from the command line.
$ sudo restart apport