Ok sorry I think I must be being really stupid.
Ok so as I read in one of the Stickies Legal means, there not legit, but that the online check for the game can't tell the difference. Which means since they are getting rejected when I try to go online with them that I did something wrong. From what your telling me that shouldn't be the case since the IVs and Nature really aren't related to anything so as long as they are with in reason it shouldn't be able to tell the difference.
So is there something wrong with the codes I am using then, I posted them above in spoiler tags. Or do I have to use Pokegen or Pokesav to do this instead of just AR? Is there some restriction I am missing?
The only thing I can think of is that I am also using a code to display EVs and IVs when I am changing them, could this have some kind of weird effect that would make them not legal?
Sorry again, and thanks again.
Edit: If anyone has any AR codes that work for them that keep things legal if with in sane values I would really appreciate it. I may just be using some botched codes.....
Big Edit: After testing a bunch of stuff I am guessing, having certian codes work and then not work, that it still checks against a database of possible IV Nature Combos.... so should I just use the Pokegen randomizer for possible combos and just go off that, could that be the issue since there not egg pokemon?