Do you warm up your writing before applying it to your current project? I do. It seems to help get the brain in gear.
Every morning, I take a few minutes to empty my brain and to get my writing in gear. I find I lose my way if I just start right in on my current project without a warm up. Try it. Either use the warm-up time to just dump what's in your brain so you'll be able to concentrate all your brain cells on your topic, or make up a list of questions or prompts and write each morning to one of them.
In either case, I think you'll find it'll make a difference if you do these stretching exercises before settling down to work on your manuscript.