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No PWM output on pins

Hello, I am trying to run the PWM module by directly writing registers.  I first verified the pin mux settings and that the module is outputting to the correct pins by using the file system interface.  Everything is fine.  Now I try to write the registers directly and it seems to take all the values, but there is no output on the pins (pin mux is in the correct mode).  I have verified that the CMPA match is occuring repeatedly, and also verified that the Action Qualifier for this channel has the correct settings.

Why don't I see any output on the pin?  Another way to ask the question: when I use "echo 1 > run" through the file system, what exactly happens behind the scenes?  What register settings are altered?

Thanks, Jamie