I created keyboard shortcuts in my extension that worked while I was testing, but don't work when I install my published version. They are:
Default: Ctrl+Shift+A, Ctrl+Shift+S Mac: MacCtrl + D, MacCtrl + S
Are these overriding something that they shouldn't be? Based on the documentation (https://developer.chrome.com/docs/extensions/reference/commands/) these keyboard shortcuts should work.
After a few days I uninstalled and reinstalled the extension, and then the keyboard shortcuts began to work. If anyone else is having this problem and they just recently published their extension, wait a few days and that may solve the problem.