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I wish I could tell you the steps to reproduce this reliably, but all I know is that this has happened to me three separate times, and a few other developers on my team have reported the same thing. Every once in a while MonoDevelop gets into a state in which double click stops working throughout the entire app. I can't double click to open a file, to select text in the editor, so jump to an error in the error list, or to do anything else that requires a double click.
The worst part is that I can't find anything to make it start working again short of actually rebooting my computer. Quitting the application and restarting it doesn't work. Logging out and back in doesn't work. Only restarting seems to work. I have no idea why that would make it start working again, and I'm sure there must be something I could do that would simulate a restart of the computer as far as MonoDevelop is concerned, but I can't figure out what that would be. I don't even understand why such steps would ever be required. What kind of state information is being persisted out of process that would affect double click? It boggles the mind...
The double-click depends on a timestamp value that's based on the uptime, and there's a known issue when it overflows int32.
*** This bug has been marked as a duplicate of bug 4470 ***
Just noting that I'm seeing this issue too. August 8, 2012
Me too - version 126.96.36.199, Sept 2012