The problem was caused because my listener in background.js was not returning a response. So the function response of my chrome.extension.sendMessage was never being executed.
I changed my background.js to be:
chrome.runtime.onMessage.addListener(function(request, sender, sendResponse) {
if (request.type == "worktimer-notification")
chrome.notifications.create('worktimer-notification', request.options, function() { });
sendResponse();
});