Thanks for your reply.

using uEnv.txt no capes are loaded on boot since we had pin conflicts with 
the emmc virtual cape. 
#Docs: http://elinux.org/Beagleboard:U-boot_partitioning_layout_2.0

uname_r=4.4.54-ti-r93
#uuid=
#dtb=

##BeagleBone Black/Green dtb's for v4.1.x (BeagleBone White just works..)

##BeagleBone Black: HDMI (Audio/Video) disabled:
#dtb=am335x-boneblack-emmc-overlay.dtb

##BeagleBone Black: eMMC disabled:
#dtb=am335x-boneblack-hdmi-overlay.dtb

##BeagleBone Black: HDMI Audio/eMMC disabled:
#dtb=am335x-boneblack-nhdmi-overlay.dtb

##BeagleBone Black: HDMI (Audio/Video)/eMMC disabled:
dtb=am335x-boneblack-overlay.dtb

##BeagleBone Black: wl1835
#dtb=am335x-boneblack-wl1835mod.dtb

##BeagleBone Green: eMMC disabled
#dtb=am335x-bonegreen-overlay.dtb

###U-Boot Overlays###
###Documentation: 
http://elinux.org/Beagleboard:BeagleBoneBlack_Debian#U-Boot_Overlays
###Master Enable
#enable_uboot_overlays=1
###Overide capes with eeprom
#uboot_overlay_addr0=/lib/firmware/<file0>.dtbo
#uboot_overlay_addr1=/lib/firmware/<file1>.dtbo
#uboot_overlay_addr2=/lib/firmware/<file2>.dtbo
#uboot_overlay_addr3=/lib/firmware/<file3>.dtbo
###Custom Cape
#dtb_overlay=/lib/firmware/EBB-PRU-Custom-00A0.dtbo
###Disable auto loading of virtual capes (emmc/video/wireless)
disable_uboot_overlay_emmc=1
#disable_uboot_overlay_video=1
#disable_uboot_overlay_audio=1
#disable_uboot_overlay_wireless=1
###Cape Universal Enable
#enable_uboot_cape_universal=1
###U-Boot fdt tweaks...
#uboot_fdt_buffer=0x60000
###U-Boot Overlays###

cmdline=coherent_pool=1M net.ifnames=0 quiet cape_universal=disable

#In the event of edid real failures, uncomment this next line:
#cmdline=coherent_pool=1M net.ifnames=0 quiet cape_universal=enable 
video=HDMI-A-1:1024x768@60e

##Example v3.8.x
#cape_disable=capemgr.disable_partno=
#cape_enable=capemgr.enable_partno=

##Example v4.1.x
#cape_disable=bone_capemgr.disable_partno=
#cape_enable=bone_capemgr.enable_partno=

##enable Generic eMMC Flasher:
##make sure, these tools are installed: dosfstools rsync
#cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh


On boot the slots looks like this:
root@beaglebone:~# cat /sys/devices/platform/bone_capemgr/slots
 0: PF----  -1
 1: PF----  -1
 2: PF----  -1
 3: PF----  -1
root@beaglebone:~#


And then I can load my overlay to a slot, but no pins are toggeling. If I 
load cape-universal instead, and do the config-pin, the pin starts 
toggeling.



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