By Serial Master do you mean Serial ISP? Which is also listed as ISP boot mode ?
With no fuses blown and no programs to load from external memory, the processor goes into ISP boot mode as the fallback, correct ? That is what the manual states, and I'm assuming I am in the correct mode for programming external memory.
On the EVK, I can change the dip switches for the ISP bits, and regardless of the settings, I appear to be in the ISP boot mode and can execute the commands I attached in my previous post.
The PID and VID should be correct since the get property commands work, but the fuse reading does not. If the PID/VID were incorrect, I wouldn't think I would have any communications at all.
We do not have the UART on Flexcomm 0 broken out on our board (we are using the signals for other functionality, so this isn't an easy option). Either way, it seems like the communication path is working correctly, since get property works successfully. The same commands should be called on the processor whether communicating over UART or USB.