MFP has my calories lower than my BMR?

Ok, I know that there are a lot of posts on the whole sedentary vs lightly active ect and BMR, TDEE and what not. Well, my BMR is roughly 1590. My TDEE is 2101 roughly, I went to a site called Scoobys fitness workshop to get a calorie amount of 1745 to lose to my goal weight. I have checked various sites recommended from here to get an average of all these numbers. Now on MFP if I set my activity level to Sedentary cause I have a desk job, it gives me 1200 calories which is below my BMR. My desk job is at home so I am up and down alot and do alot of home stuff every day. My morning routine consists of get up, clean three large parrot cages, feed various critters, straigten up and vacumn everyday without fail. I also take my dog for a walk every day without fail for 1.5 to 2.5 miles at approximately 2.5 to 3.0 mph. (Slow I know but he is 12 yo and loves to sniff everything lol) Now this is my normal routine before I started MFP so I really don't count this as exercise at all. The exercise that I've added to help with my goals is powerwalking on an incline on the treadmill for 60 minutes Monday, Wednesday and Friday. I burn roughly 4-600 calories sometimes more doing this. On Tuesdays and Thursdays I do weight training and pushups, crunches, ect for 30-40 minutes and then 30 minutes on the elliptical. Don't know how much lifting weights burns, but I'm sweaty when all is said and done. Saturday and Sunday are my rest days.
Now I was thinking of switching to lightly active on MFP which gives me 1330 calories and then just log my actual gym exercises. I don't want to eat too much or too little. I also have a borderline lower thyroid function. Not low enough to warrant medication yet but I don't want it to hinder me here, so Im thinking my BMR and TDEE might be a little lower anyways. I just fear eating too little and causing more havoc with my metabolism as that is probably what got me here. I would skip breakfast and lunch alot and binge on dinner and that is probably also what has hurt my metabolism. Now I eat three small meals and sometimes 1-2 snacks. Anyways, long post just want to get it right before getting too much further along. I was sidelined last week from doing any significant exercise cause of an injury, but I was starving on 1200 calories and unfortunately went over most days last week:( Now I am back on track and ready to get healthy!