This issue is caused by another issue:
"When opening MonoDevelop, 2 instances of one script are opened".
http://issuetracker.unity3d.com/issues/when-opening-monodevelop-2-instances-of-one-script-are-opened

If you have opened two instances of the same script in MonoDevelop, edit something in the first instance and save your changes. Remember in which line cursor was placed. Go to the other instance of the same file, edit your script on different line and save it. After saving, cursor usually jumps to the line where it was placed on the first instance.

Reproducible on MonoDevelop 4.0.1 which comes with Unity from 4.3.x version.

Workaround is to close duplicated instance.