Hey iPheuria, ok here's the screen shots.
Just to explain the screenshots, what you're seeing are the iPhone view screenshots, and the iTunes view screenshots. The screenshots from iTunes is what iTunes sees on my iPhone. The screenshots from my iPhone are what actually happens when I sync my phone. I will add apps to folders in iTunes as people normally would, then I 'apply' the changes and sync the phone. As I am syncing the phone, I can physically see iTunes adding the apps randomly across my home pages on the iPhone, not in folders (how I originally arranged them in iTunes)
If you see on screenshot number 2 above, it has some random apps in folders? but on screenshot number 3 ( the itunes view of page 2 ), you can see that iTunes shows no apps in any folders? WTF?? How is this possible? I mean I have a basic understanding of why it doesn't show cracked apps sometimes or tweaks, but I've uninstalled most tweaks.
No matter what I do, restore from backup, re-arrange apps, remove apps, add apps one at a time, it does not add sync the apps properly. It just throws them randomly across my phone, and I have no idea why it's doing this. I had infinidock and infinifolders installed, but I uninstalled them when I ran into this issue, and still the problem persists.