I guess you meant that Portugal is blinking and some other less noticeable artifacts.
I tried to publish it as video and in a video it's fine. We use exactly the same code for gif and video, the only difference is that gif supports only 256 colors, so usually you need to apply some dithering (which rarely look good) or don't use gradient colors. In your case those blinking red circles are made of gradients. Gradients use lots of colors, so it does not translate very good to gif.
I understand that my answer does not help with this problem and I am sorry about that. The only thing I can recommend is to replace red circles with some solid colors (several circles of different red, but solid). It should help with the gif, but of course it won't look as good in html5/video.
So it all depends on what is your target format. If it's gif only then just use solid colors, if it's both then the only choice is to have two different projects or something like that.
We will think how it could be fixed automatically, but anyway this is not going to be done soon enough.
cool animation btw!