Why does Android show more space used in internal storage than what adds up in the details?
DiskUsage is giving you the correct information.  Per the developer of DiskUsage:

System data consists of several things:

Unpacked dalvik bytecodes corresponding to your installed apks. If you install app on external storage, it still consumes space on your data partition.

Crash dumps stored in tombstones directory.

Any other data or settings android store on your device.


This data is hidden and DiskUsage can't easily identify how much space each of this consume. Usually (1) consumes most, so if you want to cleanup some space you may want to delete apps on external storage.

http://androidforums.com/threads/disk-usage.181747/