When the device is rooted and is running stock ROM, the OTA updates are not working properly on most devices. For example, in my Galaxy Y, when I tried to install a new firmware it stopped during the installation and rebooted on the old firmware. Then it displayed the known s*** like "The installation was not succesfull. Please try installing the firmware using Kies".
Otherwise, if your device is running a Custom ROM, you can update to the newest version without a problem.
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dimsar2013 - XDA Developers Senior Member