Gomez you are right.
Like you and Baummonster, I am experiencing that exact same problem on a number of computers, for months and months now.
As far as I can notice, this problem is present only with Eset Smart Security 7 (ESS 7) on Windows 7 64bit machines.
As you mentioned, popup windows in Interactive Mode are becoming invisible, and they can be seen briefly only when OS restart or shutdown is initiated.
I suppose it has something to do with ESS 7 UI, but I'm not an expert.
So, like you, the only thing I found to be effective is to restart the computer, which is quite silly and temporary solution. I have no problem with ESS 6 version, but with ESS 7 the problem in question is present all the time, along with some other more serious problems (but they are not for this topic).
And don't bother with making any thread cause they'll do nothing.
This is an old problem, as old as ESS 7 version, and they know about it for at least six months.
I contacted support about this same problem three times now (November, December, February), but all they could say was that Interactive Mode is not always "reasonable" (!!!) ("vernünftig", German support), and recommended that I should switch to Automatic Filtering Mode as soon as I establish all the necessary rules. But I don't want to use Automatic Filtering Mode. And even when I have to, first I have to make necessary rules, and I'm forced to run through 3 to 8 computer restarts just to make rules which will cover only the basics.
Interactive Mode worked like a charm up until ESS 7, and we shouldn't compromise with Automatic Mode. Some of us find Eset firewall to be very useful tool, and among us there are those why are able to squeeze that firewall to it's maximum, and enjoy the full potential. Why should we settle for less?
Now, after six months from my initial complaint to support (and I'm sure there are many others who did a same), I would expect that this problem would go away after some update, but it didn't.
I own 65 licenses for ESS, on 325 computers, and only six of them are set to Interactive Mode. But these six computers are experiencing the same invisible popup firewall window.
And if I have to restart even one of them, just one more time, I swear I'll start looking for alternatives to ESS, even after almost 10 years of devoted subscription to NOD and ESS.
And yes, ESS is a work in progress, and it will always be, but after how many notes to Support, and after how many months of waiting... we are still at the beginning. Where is the progress in that?