The one that I am currently noticing on http://www.pixiv.net is a banner ad that is shown when viewing the results of a search for certain images via the search box on the main page.
I don't know this webpage. Do you have to register in order to get to the location you are talking about?
Yes, you have to register for a free account.
Have you looked at this FAQ?
I tried adding the domain for those banner ads manually. It ended up also blocking non-ads.
Yeah, that will happen sometimes if they are self-hosting some of the ads or using the domains for both ads and content.