First you should have upgraded directly to 106S but tyhis is not a real problem looks like your beagle bone is broken...
Just get a new one here.
http://www.element14.com/community/community/designcenter/single-board-computers/next-gen_beaglebone/

replace it by carfully removing the old BBB form the control board.
flash the new BBB with http://www.kncminer.com/downloads/support/neptune/SD_Neptune_rc6.zip from microSD card...
to do this use a fat 16 formated sd card max 8 gb
make it booable with http://www.ptdd.com/fixboot.htm if you use microbullshit products , if you use linux use fdisk and set the boot flag on the partition table .. copt the flis from the zip file on the micro sd card.
put the micro sd in the BBB , power up the board and the BBB , it wil start and a withe , blue , green flashing light tells that flashing is finisched , remove card from beagle ,  now you sould have  version 0.6 or someting , before you connect antything , imeadatly upgrade to 1.06s vir the web interface.
When done connect the cube
the defaults are all cubes off volatage -0.0366
 , you need to reconfigure all you miner config including volatage speed , miner account , miner server , etc , if you cant do this soory you sould not have been buying this stuff , it requires some tech skills to operate an miner.
Maby I can buy the stuff from you for a good price   , but if you understand what iam wiriting I hope this is helpfull.
btw you can sevarly undervolt the cubes I have them running as low as -0.0829 volts at 500 mhz!
one miner uses around 1880 watts at all cubes at 500mhz.
if your lucky.