[readmodifywrite]

My guess is that the receiver clock glitches in some way when the MSI auto calibration runs, but it never showed up on the transmitter (and the device on the other side of the connection has never had a reception issue).

I ended up disabling the auto cal feature during a UART reception and then turning it back on when the reception is done.

SPI is definitely better as far as clocking, but MCU support as a SPI receiver is sometimes a lot less convenient to deal with.

A lot of UARTs have a synchronous mode which adds a dedicated clock signal - I've used that before out to a couple MHz.

In this application though, I'm only running 1 MHz so I really didn't think I should need a separate clock (and, it turns out, still don't).

[barbegal]

According to the documentation there is no calibration as such, the MSI clock simply runs in a phase locked loop (PLL) configuration with LSE (32.768 kHz). For example in 1MHz mode the MSI is setup to run at approximately 1Mhz, this clock then goes into a downscaler which downscales by a factor of 31 to approximately 32kHz and this is compared to the LSE clock to generate feedback for the MSI clock. When locked the MSI runs at 1015.8 kHz (32.768 * 31) so out by 1.58%.

It's also possible that the design hasn't been thoroughly tested and the PLL doesn't lock in certain conditions which could leave you with an unstable clock.

[readmodifywrite]

The lack of status bits on the auto-cal is really unfortunate.

Turning it off during a UART transaction definitely "fixes" it.

I'm somewhat tempted to do the manual calibration the HSI instead.