I am experiencing the same issue (with my Gmail account and using Google Chrome), too - although I was able to log emails going out of my Gmail to Deals previously.
I have tried uninstalling and reinstalling the HubSpot Chrome extension, which did not help. I continue to be able to log my emails to Contacts and to Companies that are associated with the Deals that I am looking to log the emails to.
I can however manually associate the emails logged to Contacts and Companies with the respective Deals.