And indeed, there was a new version of both the theme and the framework available. That seemed to fix it! Thanks splashingpixels!
I did kind of expect that there would be a notification if new updates were available but on the other hand I did not check myself which I should have.
Happily making WordPress sites again!
I have the same things as Erik describes and I use Mystile, a theme from Woo for woocommerce.
When I change to TwentyTwelve the widget works fine. When I change back to Mystile and then reload the page the widget is there until I navigate to another page. When I go back to the page it was displaying before it’s gone as well.
So,if this is happening with a woo theme as well I don’t think it’s problem with your custom theme, Erik. Not sure if that is good or bad, though…