This might by an issue with the oxygen-gtk-theme. See here. Start Monodevelop with the environment variable OXYGEN_DISABLE_INNER_SHADOWS_HACK set to 1.
In the shell:
export OXYGEN_DISABLE_INNER_SHADOWS_HACK=1
monodevelop
You can also put this as a shell script to /usr/local/bin/monodevelop. Then monodevelop is automatically started with this environment variable.
#!/bin/sh
export OXYGEN_DISABLE_INNER_SHADOWS_HACK=1
/usr/bin/monodevelop
Remember to make it executable with sudo chmod a+x /usr/local/bin/monodevelop