I haven't heard any reason to suspect that pop-under ads are a direct negative ranking factor. If it is in play at all, I'd more suspect the user experience angle. However, I'm not convinced that this is the factor that affected your ranking at all. Your analysis isn't strong enough to establish cause-and-effect as I see it.

Like Tedster said, there is not enough evidence right now to support the claim that popups have a role in ranking.

As someone with great experience in monetizing websites, lose the popups/unders. There are so many better ways to make money from your visitors than popups/unders. Take the time to get creative.

Most webmasters want to just slap on a bunch of ad code and be done with it. Different ads have different results and different ad networks will pay differently. Test different ones. Set up a daisy chain to show the top performing networks in order of highest paying first.

You can even try negotiationg with networks for a better rate. Reach out directly to media buyers to try to cut out the middle man and make more profit. Make use of your email list. Try making changes to your site that will increase the actions per visitor. More actions = more impressions = more money.

Join a community that focuses on this type of thing. Get feedback, see what ads your competition are using. Get creative. If you just settled on some network then you're probably missing out on a lot of money that another network is willing to give you per impression.

I used popunders on a website once and I felt so dirty. The pay was not worth it, I ended up removing them a week later.

Thank you for your input. I did indeed go through various revenue streams and I ended up with the single popunder. The payout is roughly 5~10 times more than all the page ads combined for my niche (300x250 ad blocks x 3). And I figured if it does not affect ranking, it actually helps page loading speed by taking on-page ads out of the equation. Does this thinking make sense?

I decided for this option for maximum page loading speed and least amount of onpage ads distractions. I did some thorough testing for maybe 5~10 different networks but ended up with just one that paid the most and being the most relevant. I frequent the forums for my niche to see if other networks come along too.

My particular niche generates very little sales and ad CTR, (low CPC too at that). I have tried to setup CPM chains such as RTB ad networks but realized that it end up slowing down the page load too much. CPM chains does offer a better payout than CPC.

Another angle that I took to remove or lessen on page ads is to avoid the Page layout algorithm. But below the fold ads simply have way too low CPM to be worthwhile. It's pocket change nevertheless but at the cost of loading speed and user experience.

How do you guys decide the sweet spot between ads loads and user experience (ranking / traffic)? Is there evidence at the time for the Page layout algorithm and above / below the fold ads?

From a user POV it's less the position of the ads and more the site design IMO. There are some sites that look great, even with aggressive ads. Others have ads in the same spots but look spammy. Finding that balance is tough, but there are lots of examples to pull inspiration from.

As for page layout, my meager understanding is that it's something like a content:ad ratio within a specific viewport.. So ads ATF won't necessarily hurt, but you need some other good stuff mixed in to sustain a nice balance. I could show you some examples of thriving sites (not mine) with side by side 300x250s at the top of every page. They have tons of other solid quality signals as well, though, so it's not cut and dry. Is it ever?

Popup's & popup ads never hurt indexing or raking of keywords.
Even so many big sites are having ads popup and own popups, all are ranking well. For spiders these popup's have different URL.