Your estimates for the calories you are burning per workout are low because they don't take into account what's known as EPOC (excess post-exercise oxygen consumption), basically fancy pants for the calories you burn as your muscles are recovering from your workout. After a hard strength workout your muscles are depleted of glycogen, their primary fuel. This will raise your base metabolism by a lot and cause your body to burn up to around double the calories you first estimated for the workout. If you don't eat enough protein within a few hours after the workout, it's possible that your body is cannibalizing muscle from elsewhere in your body to feed and rebuild the muscle that was just trained, particularly if you have muscles that you haven't used in a week or so.
I'd suggest tack on another 200-300 calories a day to your eating plan, making sure to get at a minimum 1g of protein per lb of bodyweight, and eating as cleanly as possible to minimize fat gain. While you won't see the size come on as fast as you did at first, it will make a huge difference over time.
1) eat real food - more vegetables, moderate meat, moderate fruits, less grains, less sugar, less vegetable oils.
2) exercise - moderate intensity cardio, sprinting, heavy lifting, dedicated stretching and mobility.
3) live - relax, de-stress, meditate.
Disclaimer: I'm not professionally qualified to make any formal recommendations. I've just done my homework and I'm my own guinea pig. All of my data, unless otherwise cited, comes from a sample size of n=1 (me).