I think I fixed the problem. it took me forever to trace down the actual root, and it turns out pretty simple.
in the example basic_communication, I change line 21:
while ( message.available() ) {
to this:
if(messenger.available()){
this seems to fix my problems. no more lock ups caused by an endless loop. the incoming serial data is sent to the messenger class one character at a time anyway, so it can never have 2 separate commands in buffer at the same time. so no need to use a "while" loop.