When when you compare their Godrobe activation, Satsuki's is "Life Fiber Override" compared to Ryuuko's "Life Fiber Synchronize." So it wouldn't be surprising if it turns out Junketsu hates Satsuki.
It's bound to happen sooner or later. Though after that specific scene in episode 16, I think she'll begin to understand that Junketsu really has its own will, and somehow able to convince him to do what she says with equal exchange.
