Chrome Version       : 54.0.2840.90
OS Version: Ubuntu, MacOS

I have Javascript disabled by default.  I'm signed in to Chrome in several places, including at least one each of MacOS, Android, and Linux.

Upon a recent restart of my Mac, a number of Google sites, which I use routinely and for which I had enabled Javascript, had begun complaining that Javascript was disabled.

I recently restarted Chrome on my Linux box, from which I'm filing this bug, and now the same problem has migrated there.  For example, my settings show no sign that Javascript had ever been enabled for https://mail.google.com.

So far I believe I've seen this problem for one non-Google site, but it seems mostly restricted to Google sites, including www.youtube.com.

Interestingly, sites for which I explicitly enabled Javascript after encountering the problem on my Mac now show Javascript as disabled on my Linux box, following restart of Chrome there.

But the "Javascript exceptions" list has many entries still.  It certainly was not emptied out.

I have the "Privacy Badger" extension installed.

UserAgentString: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36