Perhaps the cot is getting cold when you are feeding her and she notices the temperature change when you put her back in? I used a little hot water bottle for my DS, prepared before I got him up, popped into the cot, then removed before I lay him back down. Not too hot, you don't want it too cosy in there! it did help him settle.
Also have you looked at Harvey Karps 5 Ss, it's an extra S to Tracy's 4 Ss...it's like magic on new borns. Works very well with Tracy's BW ethos and methods too. Only real difference is the side hold and rocking which can be reduced down to a tiny movement and replaced by patting as baby gets a bit older. I first saw it on Richard and Judy (remember the show?) years before DS was born, the memory stuck with me. You can find a video on-line if you are interested. (I never read his Happiest Baby book, just used this method from memory).