At first I wasn't able to connect and upload programs from the Arduino IDE to the BlinkyBoard. I figured out that if I connected using PatternPaint and uploaded a file to the BlinkyBoard, immediately after I could upload using the Arduino IDE. Unfortunately, after I've connected and uploaded with the Arduino IDE I can't connect connect again until I've uploaded another image via PatternPaint. I'm guessing PatternPaint is resetting something to allow Arduino IDE connections again and/or something about the Arduino IDE (or the content I'm uploading) breaks things. Anyways, give this a shot if you're having trouble connecting using the Arduino IDE.
Note: Uploading blank images via PatternPaint, ie the default empty black that's there when you start the program, is apparently enough to re-enable connections. This saves me a few clicks compared to selecting and loading an actual file each time I want to upload new code.