I know this got no traction here, but I have discovered the cause and resolution - posting it here so any future troubleshooters will have an easier time then I have had. After 4+ restores, downloads, dozen of caches, resets, reboots and blank restores as well as testing on a friends iPad I have found out how to workaround this bug.
iOS6 Issue:
The scrollbar seems to bug out if the keyboard is set up like so:
- Split Keyboard.
- Keyboard moved to the very bottom edge of the screen, with NO gap - ie completely flush with the edge of the iPad screen.
The gap it turns out is the key factor here. If I leave no gap at the bottom of the splitscreen keyboard then the horizontal scrollbar will jump to mid-screen and stay there even after the keyboard 'docks/dissapears'
Solution:
Dock and merge keyboard, perform keyboard split using two fingers then drag keyboard down leaving a small space at the bottom.
(then clear safari cache)
Leaving the gap below the split keyboard allows the useless and unneeded horizontal scrollbar to stay in its place. At long last I have made peace with my iPad and Safari and can stop using other browser. This is hands down the most frustration I have had with an iPad. But, at least its fixed now.
