I, like many others, have had this problem with gmail accounts for a long time and have come to the conclusion that there simply is no fix other than to switch to a much inferior email client like Outlook, Firefox, etc. I even went to the expense of upgrading to version 9 of TheBat! Professional in hopes that it might solve the problem. I think the developers of TheBat! might have attempted to fix it in v9 because when the unknown certificate window now pops up it usually just flashes then goes away, as if TheBat! is somehow automatically clicking the Continue button for me. However, all too frequently the window still stays open until I click it.
Years ago I had an issue with a totally unrelated application periodically popping up an unwanted window so I wrote a background application that would detect it and automatically click its Close button. I'm thinking I might revive it to deal with this certificate business too. Probably many TheBat! users would be interested in a free copy :-)