Tricia said much of what I would have. Have you changed any medications? Did you eat something out of the ordinary (for me anything with the letters K F and C makes me fat overnight.) Have you had your thyroid checked? Do you get enough iodine or eat sea vegetables?
Are you insulin resistant? Are you leptin resistant? Often those two things go hand in hand.
What helps with leptin resistance is reducing the number of meals per day to 3 , adding enough healthy fats to make that tolerable, doing high intensity cardio for less than an hour per day (too much will back fire and produce cortisol, give you a hit of testosterone and insulin all at once.) and some yoga. The very act of relaxing, sitting in a cross legged position and saying "Om" relaxes the vagus nerve which has a beneficial effect on leptin sensitivity. Most people who are plump (like me) are leptin resistant and have an overabundance of the hormone in their bodies.
You can continue with STS if its working for you. Or, you could change it up and do a rotation with some circuits or whole body workouts. For me, doing 4-5 days of cardio with yoga as my strength workouts is more effective on my body fat.
Btw, it is possible to put on fat when you are under eating. My grandmother had been put on a 500 cal/day diet and put on weight. Don't buy the 'calories in/calories out' theory. Its bogus. If it were that simple then I wouldn't loose weight on more food and I wouldn't gain on less, but I do!
I hope some of this helps.