Files transferred to external HD end up in trash - very strange issue

Hi,
I seem to be having a very strange issue, hopefully somebody can help or has seen this before.
Hardware: MacBook Air, Western Digital Passport external HD, 250gb, formatted NTFS.
Software: OSX 10.7 Lion, Paragon (allows me to write to an NTFS formatted HD)
Issue Summary: I copy something to the external HD; I empty trash; the file I copied is deleted from the external HD. It doesn't happen every time.
I do also seem to have a persistent folder in trash called "WD Sync Data" that won't go away unless I re-delete it as it's also in the root of the drive. Not sure if this is related somehow.
Recently I copied 3 video files inside a folder to the HD, then disconnected the HD. When I reconnected it a while later and noticed that inside the "WD Sync Data" folder in trash were the 3 files I'd copied. I then looked inside the same folder on the root of the drive and the files were there, instead of inside the folder that I'd copied to the drive, which had vanished. If I hadn't noticed and had emptied the trash, those files would've been deleted.
It's definitely happened more than once; last time I actually deleted the files from my computer after copying, then emptied trash, and they were gone from the external HD also.
I've only found one person who seemed to be experiencing a similar problem back in 2010. It sounds similar though it could've been user error: http://www.mac-forums.com/forums/apple-notebooks/188224-weird-external-hard-driv e-trash-problem-help-please.html
Has anyone experienced this or have any suggestions?

Quick update: I ran a verify then a repair in Disk Utility as there were a couple of errors. Hopefully this has solved the issue, however it'd still be interesting to know if anyone's come across this before and what caused it?

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    [Solving Trash Problems|http://www.thexlab.com/faqs/trash.html]
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