How to Determine the different speeds

I have the same software installed on two PCs. Both are Windows 2000 Professional. One CPU and memory is larger than the other. So, it is understandable that one PC will process faster than the other. However, I noticed that one PC took only 9 minutes but the other took over 50 minutes to process an exact same file. This is definitely not proportional to their difference in CPU and memory. What steps should I take to determine why one is slower than the other?

Your immediate help is greatly appreciated.

Thank you so much.

Yan