Yeah it's a way of kindof emphasizing what you're saying. Think of it like "Isn't it!" in English, where the sentence is negative but the meaning is totally positive. You'd think this would get confusing, but in context it actually really doesn't. Not least because, while there are times where it's indistinguishable from an actual negative question grammatically, a lot of the time it's used outside of the normal grammar rules. For example, well, your example. The negative of ii is yokunai. ii ja nai would be ungrammatical, but it's an example of this usage. They attach ja nai to anything (verbs, etc) this way, and it always has this positive meaning when they do. As it happens, you can also attach it to a negative, giving you a nai ja nai?
This ja nai is a bit problematic in Japanese conversation. Depending on the intonation, it can mean positive or negative, and except among friends I wouldn't use them. In a very casual conversation, ja nai can be used with kirei- kirei ja nai! it's beautiful, isn't it! or, Oishii- oishii ja nai! It IS good/delicious!
It's more often used by female than male speakers. When it's used in the end of the sentence, with a bit of excitement, it's often times positive, although, when used with negative such as dame-not good/bad + ja nai it means negative unless it's a real question. so, dame ja nai!! is "(What you did) is bad!!"
Hope this didn't confuse you..... it's confusing ja nai? (It's confusing, isn't it!)