When you say you're swelling, are you talking about all over, or particular body part(s)??? If you're swelling in one particular spot (like the knee for example), that's a problem. If you're experiencing some swelling all over, that should fade with time.
I can't say I've looked too closely at the JM system you're doing, but I'm not a huge fan of 30 day shred and some of her other dvd's.
When you say you're eating clean, what exactly does that mean? Are you trying to lose weight, or just maintain? Are you tracking here on Spark? If so, are you getting within your ranges on most days?
You mention that you're adding muscle...are you getting tested in some way to determine this? It's pretty tough for women to add significant muscle mass, especially while trying to lose weight.
I guess I need a little more detail than what was in your original post.