Hi,
I'v been having this same problem for over a week.
Every time I update any apps, my iPad becomes completely unorganized.
Apps are out of folders, apps that I deleted are back.
It happens when I update thru wifi, and when I connect thru my Mac.
It's one big pain in the butt.
Please help.

The easiest first way to try to solve ‘unexplained’ or ‘unusual’ problems with the iPad are:-

Force the offending app to close. If you have iOS 4.2 or 4.3 double-press the ‘Home’ button to bring up the multi-task bar at the bottom of the screen. Press *and hold* any icon until they start to ‘jiggle’. Then tap the top left-hand corner of the app that you want to close. It will ‘disappear’ from the list. Don’t panic - you’ve not deleted it, just closed it. Now tap the Home screen and the multi-task bar will disappear. Re-open the iPad’s app and see if the problem has resolved itself. If not, it’s on to possible solution number two!!
Restart the iPad. Press *and hold* the Power button. After a couple of seconds a slider control will appear asking you to confirm that you really want to switch the iPad off (this is all you’ll be doing). Slide the control to accept. A rotating white ‘bezel’ will appear in the iPad screen as the iPad powers down (it takes a few seconds, just like it would if you were shutting down your PC). When the screen of the iPad has gone completely blank, press *and hold* the Power button for a couple of seconds until the white Apple logo appears and the iPad starts to power up. This takes several seconds, so be patient. During the power up the automatic screen orientation function is disabled, so don’t panic. A few seconds before the power up is complete, the iPad plays a little ‘jingle’ and then you’re back to the Home screen. Restart the iPad’s app and see if the problem persists. Apple (and Forum members) recommend that you power down your iPad at least once a week, just as you might regularly completely switch off your PC. The normal procedure of just briefly pressing the Power button of the iPad merely puts it to ‘sleep’. Most Forum members have found that one of the two methods I’ve mentioned here cure a whole bunch of unexplained problems and are an easy first step to resolving most anything that happens on the iPad.

Tim
Scotland