Heya, sorry I somehow missed your last comment last night.
Natures are tied to the PID frame, which is a separate but similar thing to the IV frame. The IV frame determines which IVs the mon you catch has, while the PID frame determines which encounter slot, nature, ability, gender it is/has and whether or not it is shiny. If you want to precisely determine which nature you're getting you will need to learn how to control the PID frame, although if you just want to brute force it you can simply chatter a different amount of times until you get the nature you want -- each time you chatter you increase the PID frame by one, so chatter once then check chatter twice then check etc., eventually you'll hit a synch frame and get the desired nature.
If you want more info I suggest you read this guide, which explains most of the concepts of standard seed RNG'ing pretty well I find.