Dang scale!!

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The scale hasn't budged for me in 3 weeks!! I'm confused by my results. Can you not still lose weight even when you go over your calories some days when you've gone under on other days? Shouldn't it still work out in the end? I don't eat back all my workout calories but figure they'd come in handy if I go out or have a splurge with a glass of wine or something.

My calories are set at 1,410 a day (sedentary, 1lb a week loss).

Last week:

Monday 1,376 (over by 34)
Tuesday 1,542 (over by 132)
Wednesday 1,698 burned 452 (extra 164)
Thursday 1,425 (over by 15)
Friday 1, 641 burned 335 (extra 104)
Saturday 1,555 burned 606 (extra 461)
Sunday (Easter Dinner) 1,930 burned 339 (over by 181)

When all was said and done I still had 635 calories left over at the end of the week. The week before wasn't as great but at the end of the week I was left with 161 extra calories. I didn't go back and look through the week before that, but it's similar every week. I go over a bit here and there but also go under on other days leaving extra calories at the end of the week. Why is the scale not budging (infact the scale has been fluctuating the same 3-4lbs)?? I started my journey 8/9 weeks ago, lost 6lbs (nothing in the past 3 weeks) and have lost inches. As of two weeks ago I lost 2" off my belly, 1" each off hips, arm, chest, and leg. I feel like I should have lost the set 1lb a week. You know how MFP comments at the end of each day how much you should weigh in 5 weeks if you eat/exercise like that day? Mine says every day that I should be down 1-2lbs a week! Am I doing this all wrong?? I should add, I've always had a difficult time losing weight. I've been told by an endocronologist (I've met with 2 over the past 8 years) that even though she can't seem to pinpoint a diagnosis (she ruled out a few things) she has determined I must have some sort of metabolic issue and she recommended I muck around and figure out what works for me and just do it! I felt like I should add this point incase this is my problem. Like perhaps if I am doing the right thing calorie wise, that perhaps I need to change something up either with what I am eating or increase exercise. I want to also add that I drink 6-10 cups of water a day, I cook most of what I eat, very limited amount of processed foods, I always do well with my protein, and eat wholegrain bread/pasta/rice. I was hesitant to post this because I was trying to give it another week or two, but am frustrated.