Did you write the shared secret during that particular instance? QPST seems to choke up writing multiple things sometimes (PRLs come to mind) Try reading, changing only the shared secret, and writing.
EDIT:
Also, there is a chance that when you tried flashing the original radio only SBF, it was fine. The BP passthrough error is most likely RSD Lite. I had it happen several times while flashing the Cellular South sbf. The fix is to place the sbf in C:\Program Files\Motorola\RSD Lite and then flash. This work around was posted in the Moto Dev forums, I'll see if I can scare up the link.