Is it only while uploading using FlashFXP ? And is it only one particular file or any upload ?
Try an alternate method of uploading the file, even just copying to another network drive if possible to pinpoint if it is in fact FlashFXP.
A good defrag might be needed if you havn't ran one for a while.
Also disable the antivirus.
FXP is probably fine because the data is not on your drive.
I suspect the problem is either the data on the drive (corrupt or severely fragmented) or a 3rd party application monitoring or accessing the data as it is lifted.
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