Hello,
I'm trying to upgrade my current cubieboard2 server to a banana-pro-based one (to improve my ethernet throughput), and I'm experiencing exactly the same situation as Gordon. (Banana Pro with external 3.5 hdd. Brand new 16Gb sd with freshly loaded Armbian jessie vanilla image - I just changed passwords & hostname, updated&upgraded and installed samba).
Just in case, I'm using a 4Tb drive (some people say that the bpro supports them when externally powered), connected to the cubieboard2 "3.5 inch hdd addon package" (but changed the 5V hdd power polarity to comply with Banana Pro's one).
(EDIT: and yes, I upgraded U-Boot today)
Thx for your help