Additional information:
I seem to recall there was an issue with SPI loading at boot. This had something to do with having to enable the spi software module in main board overlay file. Of which there has been several posts over the last few months. So see those for the exact details. So basically . . .
root@beaglebone:~# dmesg |grep SPI
[ 47.792110] bone_capemgr bone_capemgr: part_number 'BB-SPIDEV0', version 'N/A'
[ 47.802326] bone_capemgr bone_capemgr: slot #4: 'Override Board Name,00A0,Override Manuf,BB-SPIDEV0'
[ 47.826377] bone_capemgr bone_capemgr: slot #4: dtbo 'BB-SPIDEV0-00A0.dtbo' loaded; overlay id #0
There two modules must be loaded at boot, through the main board overlay file:
root@beaglebone:~# lsmod |grep spi
spidev 7564 0
spi_omap2_mcspi 11588 0
Here is the include file:
https://github.com/RobertCNelson/dtb-rebuilder/blob/4.4-ti/src/arm/am33xx-overlay-edma-fix.dtsiAdditionally, if you simply upgraded your kernel from an older image( e.g. an image that started with kernel 3.8.x ). You'll need to git pull that whole git repo, rebuild the board files, then install the ones you need. But you did not mention how you've managed to update your kernels from one test to the next. The best way to test would actually be to use two different flasher or stand alone images to test properly. Wheezy(debian 7 ) for 3.8.x, and Jessie(debian 8 ) for 4.x kernels. As some important changes have been made which may conflict between different kernels. 3.8.x may actually work fine on Jessie images, but I did personally run into troubles trying to update to a 4.x kernel on Wheezy images.