maybe one thing ... is your phone connected to pc ? the prog makes a backup to sdcard befor overwriting the org file. if the backup fails it breaks the action
No it's not connected.
I tried your app on my old X8 and there it works completely, I also saw something interesting.
On the X8 it displayed system apps with an update in a different color coding, and there was also only one entry for both locations (data and system). Also when looking at the apps stored in system it's displaying them using the application name and version number.
On the Neo there are two entries. One for the app in data, displaying the name and version number, and one for the app in system, only displaying the filename of the apk. See the attached screenshots of the two entrys for the facebook app. So it seems it somehow can't read the all the information from the apks in system and so doesn't detect that there are actually updates present. Funnily enough I do get the notification of an update for a system app when I download them via the market.
I hope this is of some help to you.