All that you are describing for the rev 5.1 MCB matches for when the 3.3V power on the Raspberry Pi is not powering the circuits on the MCB OR one of the serial drivers has failed. We saw both of these sorts of things couple times (out of over 100 boards) so starting with rev 5.2 we now have an on-board 3.3V regulator. That was a reliability improvement and also allows us to power other things like an on-board OLED display and future circuits not yet released.
We will send you a replacement MCB board and would like the rev 5.1 board back so we can use it here if it repairs.
There is some chance that your Raspberry Pi has lost it’s 3.3V output OR that output failed and led to this issue. I suggest you remove the Raspberry Pi as a first step and on your bench start it up with a typical Raspberry Pi 2Amp micro usb adapter. Then measure the ground to 3.3V on the raspberry Pi to see if the Pi is part of this failure.
Here is process for removal of the MCB:
Please send an email to firstname.lastname@example.org and in subject please say ATTN Mark and something like MCB replacement.
In that email give a physical mail address that could accept a box with another MCB.
If you happen to be in the Bay Area of California, USA we could arrange a faster swap of the boards in the next few days.
I await the email, sorry for your troubles. We do make improvements to designs and thus look at every failure. That is how we have come to put other reliability and serviceability improvements in both rev 5.2 and 5.3. It is mostly for this reason we want the broken board back.