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They are not conflicting... There is a difference between "Build and Sysgen" and "Build and Sysgen the BSP" (I even emphasized that in the blog text by making BSP bold). Never choose "Build and Sysgen" from the build menu, but you can (and often have to) select it from the context menu when you right click on your BSP root node in the Solution Explorer.

The manufacturers instructions ARE WRONG. You should never do anything else but a "Sysgen" or "Clean Sysgen" as our blog post explains.

Update: I've updated the blog post to make the distinction even clearer.