The 2 upper left circles, with the question mark in between, are just lighting artifacts, don't mind them, they disappear when lighting is built. The others are indeed what I meant. I meant just the parts that are obviously much darker, on both the wood, and the yellow material. I didn't have much time for it lately. But when I have time I will either try to unwrap one of my models correctly by hand (to see if it looks ok then), or try to remove the code portion that rotates the islands out of the smart projections script. (If you have any tips on that, very welcome of course.)
I'll let you know if this works out, if it does not I'll email you one of the models in the screenshot, the testcase is indeed just a part of a model, thought that would be more practical.