Had a similar problem following the same tutorial, used Emile's answer, the 
DT overlay loads every time.
To check:
cat /sys/devices/bone_capemgr.*/slots

root@beaglebone:~# cat /sys/devices/bone_capemgr.*/slots
 0: 54:PF---
 1: 55:PF---
 2: 56:PF---
 3: 57:PF---
 4: ff:P-O-L Bone-LT-eMMC-2G,00A0,Texas Instrument,BB-BONE-EMMC-2G
 5: ff:P-O-L Bone-Black-HDMI,00A0,Texas Instrument,BB-BONELT-HDMI
 8: ff:P-O-L Override Board Name,00A0,Override Manuf,BB-SPI0-01



On Wednesday, June 17, 2015 at 12:39:14 AM UTC+10, Brendan Merna wrote:
>
> I'm trying to  enable SPI on boot up on my Beaglebone Black. I followed 
> the wiki link below under the title 
> SPI1 D1 Output and D0 Input
>
> I created the .dts file and compiled it. I then moved it to /lib/firmware/ 
> and then enabled the device overlay tree. Finally, I changed the uenv.txt 
> file by adding the text shown and I removed a pound sign at the end of the 
> document. I did this because the boot command to enable the SPI wasn't 
> working and I thought it wasn't reading the last command because of the 
> pound sign. Unfortunately, now that I removed it, I reset my Beaglebone 
> Black and it gets stuck in a state with the Power LED and USR0,USR1, USR2, 
> and USR3 all stuck on. No blinking and my computer doesn't recognize its 
> there. I'm powering through the USB port and have tried resetting and 
> powering down numerous times. This same state keeps coming up. Can anyone 
> help?
>
> Tutorial Link:
> http://elinux.org/BeagleBone_Black_Enable_SPIDEV
>

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