As far as I checked with both the files, the placement of lines in
different columns happens with the Office 2003 file only when the file
is opened in Open Office as tab separated. If the same file is opened
without being considered as tab separated (neither by any other
delimiter), it shows up similar to how your second file edited with
Excel shows up.

I suspect a change in how your file is delimited between the two files
and I very much doubt whether this can be considered a bug as it might
be a cause of file format change between the two.

-- 
OO calc adds spurious columns to Office 2003 XML files
https://bugs.launchpad.net/bugs/255734
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