Can a virus window popup occasionally on a clean system?
Yes. If the system is web browsing, and the system is clean of malware, the web content may still contain HTML code that causes the browser to pop up a window. This can happen even if the system has no malware on it.
Are my virus checkers mistaken and I have a virus?
Maybe. My guess is, no. However, I'm basing that on rather little information, and so I could be wrong.
One thing you may wish to do is to run Process Hacker or Process Explorer to confirm that the offending advertisement is coming from the Chrome process. Both software has a way to identify which process a window is coming from. (Process Hacker involves dragging an icon; I think Process Explorer involves clicking on an icon.)
If the problem is indeed within Chrome, you might want to try erasing your Chrome Profile, or uninstalling Chrome, and seeing if either approach fixes the issue. Even if that doesn't fix the issue, the good news is that the rest of your system is likely uninfected.
How can I get this to stop?
Ultimately, the answer is: you have to apply a solution that fixes the problem.
Let me give a hypothetical cause. Your ISP is modifying HTTP traffic. Before scoffing at such an unrealistic idea, know that major ISPs have been known to do that (search for "super cookie"). It could be that some advertising network is involved, as advertisement networks are known to be used my malware distributors. IF that is the case, changing settings on your computer is unlikely to fix the problem.
If your router firmware had a vulnerability, and your router is now infected, then changing settings on your computer is unlikely to fix the problem.
Those are just two examples. Modern systems are complex enough that there are lots of pieces, and so lots of potential areas where something could go wrong. So, there is no one simple series of straight-forward steps that will guarantee the quickest resolution to this issue. You can follow some advice, which might work, or might not. If some advice resulted in the problem still existing, that doesn't mean that the advice was bad/senseless, because sometimes some possibilities are basically just as likely as other possibilities, especially when there is little solid detail available.
Your best course of action is to start following some good/likely advice, like what Ramhound suggested, but know that this might take some time/exploration to fully resolve, especially since we are talking about experiencing the Internet (which involves multiple computers/devices, networks, companies, etc.) If simpler fixes aren't resolving the issue, some "more advanced" steps may eventually be needed, like network sniffing and reviewing the HTTP content/traffic. Prepare for the possibility that this might take some time (and effort) to get resolved. (Or, if you're sufficiently fortunate/lucky, it might not.)
A virus will only be detected if there is a signature for it. Just because you don't find anything does not mean your not infected. If Chrome is the only browser that is doing it, delete the chrome user profile, problem solved. – Ramhound – 2015-05-15T23:28:15.503
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Can you share screenshots of these popups? What process do you kill? The one associated with that specific Chrome tab where this popup is displayed? If it's just a browser popup then dismiss it and forget about it. If it irritates you check whether Chrome's popup blocker is enabled or not. Also the answers to this recent question might help. Last but not least I'm sure there are far better popup blockers available as extensions.
– Karan – 2015-05-16T02:34:23.483