It surprised me too. But it really happened. I had the same same symptoms as OP. Clicking on "Run" would make MO blink and then nothing. Reading the log file there was a line for each time I clicked on "Run" that meant plugins prevented programs from running (I don't remember the text sorry). So I did what I explained and, miracle, I could run programs through MO. Or I didn't understand OP and am completly H.S., in this case sorry.