Have you checked the keyboard shortcuts box on the bottom of the extensions page to verify that your suggested keys are actually set there?
I ran into a similar problem...when I loaded my unpacked extension for development the suggested keys were not set, even if the key was available and defined in the manifest. I had to manually go and set the keys myself in the extension page. I'm not sure if this is the best solution, but I couldn't find any answers from searches. Also, when I published my extension on the chrome store, the suggested key's worked and were set automatically...so this seems to happen in dev mode only.