Thanks for responding Greg, I did find a solution. As soon as I posted the question, I did another search on the internet and found the answer. I have already tested it.
What I found is that when using .csv in Python the output file needs to be opened in binary mode.
My code was like this: open('DataFileComparison', 'w')
When I set the file mode (sorry, not sure exactly what to call it yet) to 'wb' it worked fine, no extra rows.
The code is now: open('DataFileComparison', 'wb')
Dale,