So has this just started or has this been a problem form day one? did you reboot the computer or close and restart SW? Sometimes the graphis cards get tired and need to be refreshed by turning of and rebooting. we need to know some more detail to help out.
This has been happening since Solidworks 2009, and now with 2010. Rebooting the computer or restarting Solidworks isn't necessary since all I need to do is close the sketch and open it again.
I found this thread that identifies the same problem: https://forum.solidworks.com/thread/25881
Try this test:
Extrude a cylinder in the front plane, then start a sketch in the top plane. Select one edge of the cylinder and convert entity. Then try to select the other edge.
Sometimes I can't select the second edge.