Why 2 same files have different size on NTFS?
This is probably due to how Paragon driver handles native NTFS compression. If I understand their docs correctly, it can un-compress on-the-fly, but cannot actually write the file back in compressed state.  

From their faq page:


How does the NTFS for Mac® driver handle compressed files?
NTFS supports its own compression feature. It is impossible (without a special copy routine) to copy compressed files or directories “as is” - because after the reading step we get the uncompressed file or directory. However, if the destination folder is compressed (on an NTFS partition), then the file or folder will be compressed too.


You can confirm your suspicions from Windows, by using standard Windows tools:
https://technet.microsoft.com/en-us/library/cc976811.aspx
(Unfortunately, I haven't found any tools that can confirm it from Paragon)