I have never, ever had any problems transferring files between systems using versions of NTFS. NTFS is one of the things that Microsoft has done well in. Files and partitions created with a newer version of NTFS are (AFAIK) 100% backwards compatible with systems running older versions.
If you're using anything but an NTFS formatted external drive then all NTFS-specific attributes and metadata is transparently stripped while copying. This is normal and expected. So, if they were transferred via CD/DVD or over the network then NTFS is not the culprit. And, based on the fact that NTFS is backwards compatible with itself, I'd pretty much rule out NTFS altogether (barring filesystem corruption, of course; run chkdsk to be sure)
The best duplicate file finder program I've found is called, appropriately, Duplicate File Finder
. Another program that may be helpful is called Directory Toolkit
. Duplicate File Finder is free, whereas Directory Toolkit is not.