So, I have two TB48s. One shows 5700mAH of capacity, but the other shows 5444mAH as the capacity.

I've tried a deep cycle using the Inspire (fly until it lands, then leave it on until it shuts off) and then charge back up.

The battery has ONE charge cycle (it was new before I did the firmware update and the deep discharge).

Is this thing defective?

Probably not. LiPo batteries will differ a bit and yours is not "broken" in yet.

//Ulf