I'm switching to flat mode because it is easier to tell which response the person applies to for me. Threaded mode you still have to scroll down and look especially if you go directly to the post, or if you're not sure of the respondee due to content or some other reason. Flat mode has the persons name, much better, no confusion, no guessing.
As to the color difference, if I'm not mistaken what seems to change the color for me is just visiting the forum, not reading all the new posts in the forum. At least that is what I have surmised because frequently I will visit and not read all the new posts because of time and then when I return the posts I've not read aren't "highlighted" like other new posts that have appeared. Then you have to remember which ones you've read and so on and it gets too confusing, especially with limited time.
I know that you do all you can to make the board easy to use Pilgrim and I hope my observation wasn't taken as a complaint, I appreciate what we have available to us and all the work that goes into it.