The explanations here were very helpful to me, though in my case, it was FireFox causing the trouble. In the end, the solution was very simple:
(1) Go to "Tools" in the menu at the top of the FireFox window, then >Settings>Privacy and Security and scroll down as far as the big heading, "Cookies and Data," which will appear in the center of the screen. Now look over to the right,* and you will see "Clear data." I clicked on the button with "Manage Data," which led to "Manage Cookies and Site Data." Then I clicked on "Remove All" and finally, on "Save Changes." Under "Manage Cookies and Site Data," there was a long list of sites, some of which I recognized, and others, not. That is why I didn't do any experimenting to see which one might be involved in the problem, but chose to get rid of all. The hateful three (in my case) boxes obscuring most of the space on the right side of the monitor (forcing me to keep moving the FireFox window to the left and shrinking it so I could see the directions from here that I was trying to follow) did not magically disappear when I hit "Save Changes," but after I restarted the computer (or did I merely restart FireFox? I forget. Anyway, in the end, when things were restarted, the fake alerts were all gone and have not come back. At the worst, restarting your computer should do it.
*If you are having trouble seeing "Clear data" and the rest, put the cursor arrow in an empty space at the very top of the FireFox window, hold, and drag the whole window over to the left, exposing the part that was hidden behind the fake alerts. (For newbies: This technique works with any file or window, so far as I know.) You may also have to do some finagling, resting the cursor on the very edge of the FF window until it turns into a two-way arrow, and then pulling it to make the window narrower, or hitting Control and then the minus sign on the keyboard to shrink all the writing.
Words cannot express what a relief this was and how grateful I am. I hope this post will help people who are using FireFox. In my case, the popups appeared immediately after I clicked on a link in someone's comment in a thread on Yahoo mail, though it originally came from a column in some newspaper. I wish I could remember what it was so as to warn others away, but I can't.