In summary, Arduinos that have programs that stream out serial data are very difficult to program / work with, even outside of the IDE, as evidenced by minicom's issues.
Probably the best way to handle this is to insert a pause in your setup before initiating the serial setup and such.
Another (and possibly better) alternative would be to set things up so that you can send a command to start/stop the streaming (and store the setting in the EEPROM); that way, you could turn off the streaming before doing a new upload, then re-enable it for your testing.