I just tried it. I think the problem is that iTunes 11.1 beta only sees the first page of 9 apps.
So in iTunes I added an app to a folder which already had 13 apps in it on the iPad 2. The apps were organized as 9 on page 1 and 4 on page 2.
Then I synced. iTunes
does sync the app. However, what I now get is 3 pages for that folder on the iPad 2. I have the same original 9 on page 1 and the new single app on page 2. The other remaining 4 apps are now on page 3.
ie. 9 + 4 (two pages) plus add one app = 9 + 1 + 4 (three pages).
However, if you go back to iTunes, it still only sees the 9 apps on page 1.
Another bug:
On iTunes, I have main 4 pages of apps and folders. On my iPad 2, I only have 2. The extra 2 pages in iTunes are filled with apps that are in the extra pages of the folders on my iPad 2. WTF. So, I think this is directly related to your bug.
Look at the 4 pages on my iTunes screen.
However, there are only 2 pages on the iPad 2.
The apps on the extra pages of my iTunes screen seem to belong to the extra pages within the folders on my iPad 2.