Do you see:
book1.xls:1
and
book2.xls:2
If you do then this isn't really two copies of the workbook. It's just two
views (or windows) into the same workbook.
You can select the one you don't want to see, then hit ctrl-w to close that
window.
Then save the workbook or you'll be doing it again!
Debra Dalgleish has some instructions with pictures:
http://contextures.com/xlfaqApp.html#TwoWindows
This can be caused by using:
Window|New window
(maybe followed by window|arrange)
It can be quite useful to see different ares of the same workbook (even same
worksheet) at the same time.