I was having that issue with the Flex Beta. Only way to fix it was to disable the Flex mobile substrate addon (I used iCleaner Pro to do this but you can also use sbsettings) and respring. Once the springboard was back I would open the offending app to confirm it was fixed, then re-enable the flex MS addon.
Flex caused this issue every time I turned the device off then back on. Temporarily disabling it off then back on (with respring in the middle) always fixed the problem 100% of the time.