IGNORE THIS POST, now that BIOS 1.03 is released. Have seen enough posts on asking firmware 1.03 fix... For the impatient, perform the following hardware fix to shun two circuit paths (Both "always_on 3.3V" and "always_on 5V" power rails supply power to Arduino 101 all the time.) <-- add two bypass links (pink lines) Naturally YMMV and take your own risk on warranty issues and it's for hard-core geeks only. ccs_hello
This would seem safer using a blocking diode. I can't imagine tying 3.3v to a 5v rail is a good thing.
Modified my OP to read (Both "always_on 3.3V" and "always_on 5V" power rails supply power to Arduino 101 all the time.)