Here's the symptom as one user described it: The ad itself is not visible, but when the video reaches the yellow ad markers (and why are those visible if the ads are blocked?), it flashes a black screen four times with the message "advertisement" on the top left and then it resumes playing the video.
This is an oddity peculiar to Crunchyroll.com. Here's how one of the bright folks in the open-source ad-blocking community explains it:
It isn't possible to make in-video ad-blocking seamless, as on other streaming sites such as Youtube.com. Making it seamless like YouTube might be possible and might not be. Crunchyroll is not fetching and playing video ads the way YouTube does. Crunchyroll first loads a placeholder for video ads in an object like an iframe and then pulls the video ad. Once the video ad is done playing or if the user skips it, the site pulls another object like an iframe to play the video you wanted to see. The custom filter for Crunchyroll.com only blocks the video ad, not the iframe that loads separately for it.
But the difference is only two to four seconds. It won't be seamless as YouTube, but you won't have to see any video ads for the price of waiting a few seconds until the episode you want to watch loads.
The flashing is the iframe or other placeholder object being loaded for the video ad and then bypassed by the custom filter.
Anyway (he adds), Crunchyroll isn't free. KissAnime and 9anime offer free service without any video ads. He suggests watching anime there instead. :)