Migrating to the STM32F405ZGT6

Ahh - the interpreter isn't multi-threaded so it relies on having short functions that finish relatively quickly. When you get data from serial it goes into a Queue, and that queue is handled in the 'idle' loop - so it's expected that what you're doing there won't work.

The best bet is to use on('data' as you say. If you post up details of what you've got then I can try and see why it's not working?

As a start, you could try:

var dataLine = "";
Serial6.on('data',function(d) {
  dataLine += d;
  var idx = dataLine.indexOf("\n");
  while (idx>=0) {
    var command = dataLine.substr(0,idx);
    soStuffWith(command);
    dataLine = dataLine.substr(idx+1);
    idx = dataLine.indexOf("\n");
  }
});