I had the same problem: everything worked just fine, close, restart Windows, run Eclipse (which loaded the last workspace with the last project open), but although there are no "errors" in the Problem window, nothing runs when I do Alt+Shift+X, J (shortcut for Run Java Program).
Introducing a syntax error in the code correctly reports the error, as well as the error going away when the syntax error is fixed.
Cleaning the solution had no effect.
Dropping to the command line, Maven still compiles everything perfectly. Inspecting the Eclipse Error Log window I did find many warnings, but no errors. Finally I tried per chance the Run > Run Ctrl+F11 menu option, and then it ran the program just fine as expected.
After that the console displayed output as before, and now the Alt+Shift+X, J shortcut, as well as the Alt+Shift+X, T shortcut (for running JUnit tests) started to work as before!
Now, after running a program or a test, jumping to the console with Alt+Shift+Q, C works fine again. I can only conclude that for some reason, the console was not initialized, but in addition to that, the code really did not run since file output that the program generates also did not happen.