size on disk

• du gives two different results for the same file

When you run du without the --apparent-size you're getting the size based on the amount of disk's block space used, not the actual space consumed by the file(s).
This is a common problem when you put the same data on 2 different HDDs. You'll want to run the du command with and additional switch, assuming it has it - which it should given these are Linux nodes.
http://unix.stackexchange.com/questions/106275/du-gives-two-different-results-for-the-same-file

• What’s the difference between my file size and the size on disk?

When you right-click to view the properties of a folder, the property sheet includes two values: Size and Size on disk.
The values reported by Size and Size on disk aren’t meant to be a byte-for-byte accounting of the total impact of a directory on your disk free space. They’re just a rough estimate based on the assumption that most files are of the boring variety. By that, I mean no hard links and negligible use of alternate data streams. If you have a directory with numerous hard links—such as the Windows directory itself, for example—the values will be way off.