The particular BoB I'm playing with doesn't seem to be defective as such. (It's almost too simple not to work). I'm commenting on the difference between I/P and O/P 'scope wave forms. To test it I'm feeding it with a 555 astable on a breadboard producing close to a 50/50 square wave. I'm varying the frequency with a simple change of C. What comes out is 'orrible!
What I find odd is the channels outbound from the PC pass through 74HC14s before they get to the optos. No such buffering/inverting on the inbound direction.