Hi Michael

 > When I do 'cat value' in the gpio48 directory, I get 1. I should get a 0 
since the pulldown is enabled.

> To my experience the 'cat value' not always reflects actual level on the 
wire.
and
> Should modifications in the DTO reflect in the file interfaces and on the 
physical pin itself,  
DTO modifications not always change the pinmux settings or pin state. (For 
example uEnv.txt settings might override them)

I concluded useless to study roots of every case, as well as got tired from 
checking pinmux settings and wire levels every time I connect new device to 
the system, and wrote small linux utility showing the punmux settings, GPIO 
configurations, and wire levels(if GPIO receiver enabled).
Maybe it will be helpful in your case, to understand what is where:  
www.academ.org/~sv/epc/pinmux.pdf

Serge



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