I am using the tablesorter plugin (http://tablesorter.com) and am having a problem with column widths in IE7. It looks fine in Firefox and sometimes in IE7.
Here's a screenshot of the problem:
and here's how it's supposed to look:
This is a common layout problem in IE. If you are using CSS to style the columns width, also add the column widths to the td tags. Set the first column to a percentage that will try to suck up most of the space, like 50% or something. The first column width will take everything that it can and the other columns will abide by their static width.
Can you perform a checksum on your original file, and the uploaded file and see if there is any immediate differences?
If there are then you can look at performing a diff, to determine the exact part(s) of the file that are missing changed.
Things that pop to mind is beginning or end of stream, or endianness.