>From the BBB wiki page:

Onboard HDMI
> The onboard HDMI driver uses the LCD pins. They are still connected to the 
> expansion header, but in some cases, they could cause an LCD cape to have 
> some noise issues unless the cape has a buffer.
> A buffer should take care of this issue. If you want to use these pins as 
> GPIO pins, you may be limited in speed due to the capacitance caused by the 
> loadig of the pins by the HDMI driver.
> They should function fine in most applications.


 

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