You're right, closing a serial port possibly does affect some settings, so I reran my stty while download.c was waiting for an empeg to connect to.

My guess it is the 'min = 4', which in compination with -icanon blocks your read until there are at least 4 characters in the buffer. But you probably also want to turn off the nl -> crnll conversion (onlcr). As well as imaxbel, which flushes the buffer when a ^G character is sent.

For the rest I can't really quickly find anything else that might affect things.