960 has its own rating. The points awarded are not influenced by an opponents online chess rating. It doesn't matter that someone is higher rated and therefore "better" in standard chess, because they might totally suck at 960.
It's definitely a good idea to keep the ratings separate. They're two different games. However, I was surprised to note that my seek for my first 960 game required me to include my "rating" in the range of possible opponents - by which it meant my normal chess rating of 1618, not my 960 default rating of 1200.
i don't necessarily think this is true, but i do think that the ratings have to be seperate, and there wasn't a really good way of porting ratings over (new people would still start with 1200, etc).
The bug I mentioned also seems to show someone's regular chess rating on the "open seeks" page for a 960 game, even if their 960 rating is different. I'm sure this has already been brought up - some bugs are expected with any new development, especially one as major as this.
By the way, Erik, since you posted in this thread: THANKS for the huge new feature! This is really exciting and I know it took a lot of work.
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