Hi, I have the same problem with the same device tree overlay. 
The setting of the PRU works when I put added the PRU pin mux in the 
am335x-boneblack-emmc-overlay.dts but not when I insert it to slots.

Here is my device tree that I add to the am335x-boneblack-emmc-overlay.dts.

/*
 * Copyright (C) 2015 Texas Instruments Incorporated - http://www.ti.com/
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License version 2 as
 * published by the Free Software Foundation.
 */

&am33xx_pinmux {
    gpio_pins: gpio_pins {         // The GPIO pins
             pinctrl-single,pins = <
                0x070 0x07   // P9_11 MODE7 GPIO output pull‐down
                0x074 0x27   // P9_13 MODE7 GPIO input pull‐down
             >; 
          };
 
 
 pru_cape_bone_pins: pru_cape_bone_pins {
  pinctrl-single,pins = <
   0x1a4 0x05   // P9_27 pr1_pru0_pru_r30_5, Mode5 output pull‐down
            0x19c 0x26   // P9_28 pr1_pru0_pru_r31_3, Mode6 input pull‐down
  >;
 };
};



&ocp {
   helper {
             compatible = "gpio-of-helper"; 
             status = "okay"; 
             pinctrl-names = "default";
             pinctrl-0 = <&gpio_pins>;
          };
    
};

&pruss {
        pinctrl-names = "default";
     pinctrl-0 = <&pru_cape_bone_pins>;
};

I'm not sure what is happening. But I am using kernel 4.4.9-ti-rt-r26.My my 
PRU code loaded to the pru is just blinking LEDs from GPIO P9_11  and 
pr1_pru0_pru_r30_5. However, only the P9_11 blinks. When I "sudo cat 
/sys/kernel/debug/pinctrl/44e10800.pinmux/pins", the pins corresponding to 
the PRU pins are not changed. Why do you think this happens?


Thanks


Kister


On Monday, April 4, 2016 at 10:55:45 PM UTC+8, RobertCNelson wrote:

>
>
> On Mon, Apr 4, 2016 at 9:51 AM, Xsentius <[email protected] 
> <javascript:>> wrote:
>
>> Oh, that is a very precious information, I really appreciate it. 
>>
>> So is there a way to see updates? Do you recommend me to go back to 3.8, 
>> if it is stable?
>>
>
> Correctly set them in the overlay and don't worry about it..
>
> Regards,
>
> -- 
> Robert Nelson
> https://rcn-ee.com/
>

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