If both video outputs is from graphics card, one could be 1080i the other could be 1080p, graphics card could output at different refresh rates.
If using a single output from pc with HDMI splitter, this gurarantee the signal will be exactly the same, hopefully 1080p, and the same refresh rate (1080p 60hz).
Check with your graphics settings about refresh rate and resolutions.
Maybe internet search might help.
https://www.google.com/search?q=change+refresh+rate+windows+7
But, changing refresh rate while cloned may sometimes change refresh rate of only one of the 2 monitors. Single output with hdmi splitter may be more reliable if you want the same exact signal to go to both monitor and capture card.