I just installed RAMPS 1.4 on my Prusa i3 and uploaded the marlin firmware and everything appears to be working correctly apart from the speed of the printer, The printer is going i would say 3 times faster than it was before the upgrade and the slic3r settings haven't been changed. They still are set to 60mm/s.
Any ideas as to how to fix this?
If the steps/mm were wrong, the printed objects would be the wrong size. If they are the correct size, then you know steps/mm is correct.
What I would look at are the maximum speeds you have set in the firmware. Your G Code can ask for whatever it wants, but your firmware could limit your speed to less than is in the G code. I suspect that your earlier firmware had lower maximum speeds than what marlin is giving you.