What is the difference in using PCM MSB and PCM LSB?

MSB and LSB are two different ways of sending 16-bit PCM samples over the network. The difference is in the byte order (most vs. least significant byte first).

The setting must be compatible to the communicating partner. For a communication between two Barix devices (e.g. STL link) it does not matter what you choose, but configure both to the same value. If you are interfacing another equipment (e.g. a PC), your selection must be compatible to it.

MSB is the network standard. LSB is usually generated by PC programs.