I finally understood why I was not able to use GPIOs on my am437-gp-evm: the dts file provided in Arago "dylan" is incomplete: GPIO banks 1 and 2 are not declared, so the GPIOs numbering are not respected. This is in the 3.12 Linux kernel.
Signal marked as GPIO3 are in reality mapped on gpio32 and GPIO5 on gpio96 (but only after turning it on, it is off in the DTS).
The issue seems to be solved in "Daisy" (kernel 3.14) , but I did not have the opportunity to check it out already.
Michele