The problem is, as you say, on your end. I dont think it has been addressed in the latest update.
I)t did happen to me quite a bit. It was after the introduction of the https sites. Lazy, or bad programming on those sites which updated, left a mixture of secure and insecure content - hence the unnecessary popup.
IE interacts with Edge, it seems. The advice I was given at the time, (should you find it happening again), was to open Internet Explorer - Tools - Internet Options - Security tab - Custom level.
In Settings: Under "Display mixed content," (About half way down) select "Enable". Apply and OK and then exit
This certainly worked for me.