If by 'main build', you mean the the non-bootloader USB connection, then no, that works fine.
I have just tried it again, upgrading to r13396 at the same time
and it worked fine.
However, disconnecting from the the bootloader USB is still problematic. Sometimes it flashes an ATA error (too quickly to read the number), but mostly it just hangs as previously described.
EDIT: I also just replaced the bootloader on the very slim chance it was corrupted - no change. Could this be a strange hardware version problem?