It could possibly be a discrepancy between the times between the server and your computer due to the weird daylight savings time thing that happened this year. I'm not really sure how this would affect anything, since I'm not particularly familiar with the upload script, but since you mentioned time, that's one thing that came to mind for me.
If that's the case, try uploading the files on Monday, since all of the daylight savings time issues will be sorted out by then.
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thanks redshoepaul
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