Hi Mike, yes BGA is not so easy to handle as the LQFP, it could be tricky for guys new to it. How many boards do you manufactured? do they behave the same during JTAG debugging? By examining this we may have a gross estimation that if it's a hardware problem, I guess the SMT mounting vendor should also be able to assist you to examine it, with X ray validation machine.
Back to the software, I'm thinking that you can try the following steps 1) to boot our default released u-boot binary for BF609 and see what happens 2) do necessary porting for your board on u-boot and try to boot. I'm suggesting you to use u-boot directly instead of customized bear metal code because this forum is more familiar with u-boot so we are more likely to share helpful thoughts during your Jtag debug, and it's verified on bf609.
