Problem:
The culperate was a "Apple Script / JavaScript Widget" trigger. The following code was being run every second which caused Google Chrome not to stay closed:
tell application "Google Chrome"
set window_list to every window
...
end tell
Solution:
Only run the script if Google Chrome is running. Modify code like so:
set appName to "Google Chrome"
if application appName is running then
tell application "Google Chrome"
set window_list to every window
...
end tell
end if