Hi Shell, Welcome to 3FC. My first thought was, Are you SURE you're not losing weight?
Like you wouldn't know. You're doing all the right things, that's for sure!
I'm not sure about the exercise/muscle stuff, my personal experience has been that exercise doesn't affect my weight at all, I just do it to hopefully one day see results
I do know that it is tougher to lose on Atkins the times you go off/on. Not sure how steady you've been in the past, but I have a girlfriend who is on for a week, then off for a couple, and when she does buckle down and get serious, it's really tough for her to lose.
What's a typical menu for you? Are you using the Atkins shakes/meal replacement bars? A lot of folks (myself included) have found that the supposed 2 carbs (or "advertised" carbs. Grrrrr) are enough to kick you out of ketosis. I've had better luck going back to the pre-net carb diet.