The baud rate and related configuration was not changed from the original setup as I wanted to test this logger with the minimum of changes to the config file. Also, about half the time, data are stored on the SD card, while the rest of time I get the error message. It definitely seems that this is somehow related to the serial connection, but the data are observed in parallel on a terminal program at 9600 baud so not sure why this logger is objecting to getting serial data consistently.
If there was a baud rate issue, I would not think that the logger would crash and stop logging altogether, I would think that it would just log garbage characters, like the terminal programs do when they interpret data at the wrong data speed.