I've been using spi2  quite extensively in python:
from spidev import SpiDev as SPI
and it works fine for me.
> ls /dev/spi*
/dev/spidev1.0  /dev/spidev1.1
> 
> sudo cat $SLOTS
 0: PF----  -1 
 1: PF----  -1 
 2: PF----  -1 
 3: PF----  -1 
 4: P-O-L-   0 Override Board Name,00A0,Override Manuf,BB-BONE-PRU
 5: P-O-L-   1 Override Board Name,00A0,Override Manuf,BB-ADC
 6: P-O-L-   2 Override Board Name,00A0,Override Manuf,ADAFRUIT-SPI1
> uname -a
Linux BBB4 4.1.15-bone17 #1 Wed Dec 16 17:39:16 UTC 2015 armv7l GNU/Linux
> 
> lsb_release -d
Description: Debian GNU/Linux 8.3 (jessie)
> 
I could post my tbo file if you think it would help, but I don't think I 
changed it much besides playing with the clock rate
and making sure d1 and d0 change on negative edges of the clock (i.e. 
commenting out spi-cpha;)
Have you checked your pins carefully; for example, the clock should be an 
input not an output; I've never figured this one out.

I load the overlays using a service that simply calls a shell script in my 
bin directory:
#!/bin/sh
cd /lib/firmware
echo BB-BONE-PRU > /sys/devices/platform/bone_capemgr/slots
echo BB-ADC > /sys/devices/platform/bone_capemgr/slots
echo ADAFRUIT-SPI1 > /sys/devices/platform/bone_capemgr/slots
> 
I could also post the service, but it is very straightforward and simple.

My pins are defined as:
pinctrl_spi1_pins {
pinctrl-single,pins = <0x190 0x33 0x194 0x33 0x198 0x13 
0x19c 0x13>;
linux,phandle = <0x1>;
phandle = <0x1>;
};
When I do >sudo cat $PINS, their values are verified:
pin 100 (44e10990.0) 00000033 pinctrl-single 
pin 101 (44e10994.0) 00000033 pinctrl-single 
pin 102 (44e10998.0) 00000013 pinctrl-single 
pin 103 (44e1099c.0) 00000013 pinctrl-single 

I hope this helps a bit.

>

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