On Mac, if you have an app open and you try to launch it again, the Mac just switches to the open app. You can force it to open a new instance by passing the option "-n" to the launcher. In a terminal, run
open -n /Applications/MonoDevelop.app
Note: MonoDevelop is capable of opening multiple solutions. To do this, simply uncheck the "close current dialog" checkbox in the "Open" dialog, or hold down the control key when clicking on one of the recently opened projects in the Welcome Page.