Scales are just instruments of torture and muscle/fat ratio, which translates into how slim and toned you actually look and feel, is much more important. Pag this definitely sounds like something you should bear in mind, given your clothes are fitting better, even though you say your weight has increased!
However, regular exercise is too often interpreted as a free pass to eat too much! I'm not saying this is definitely you OP but a two mile run, sorry to say, won't burn that many calories...probably around 200, possibly less, especially if your body is well used to doing it so it isn't really a challenge...very easy to wipe out those calories with just a couple of chocolate biscuits!
Re weight loss and age, the reason it is harder to lose weight as we age is because muscle mass deteriorates, particularly post menopause. Muscle burns more calories than fat, even at rest, so with less of it, metabolism is decreased. Cardio is great but as important, if not more so, is regular, proper resistance training to build and maintain muscle. Then you should be able to eat as much ad you used to without piling on the pounds 
. Forget the idea of "bulking up", this just does not happen to women (or at least not without vast amounts of protein, hugely intensive training, plus, usually, chemical assistance). Get some proper instruction and start lifting weights regularly, you will see the difference.