Solved!

I'm sorry to say that after all of this discussion, it was just a stupid programming error. I leapt to the wrong conclusion to quickly.

At some point I had made a change in the program to make it set the output baud rate to zero. My hope was that even if it didn't actually turn off the output, it would make it so incomprehensible that any status messages that the empeg was giving on the serial port wouldn't contain any real letters and be interpreted as commands to the wideband.
It worked fine on the bench but for some reason stopped working when I moved it to the car (perhaps because that was the first reboot since I had made the change).
I don't even know what the behavior is supposed to be if you try to set the output baud to 0, I was just trying it out.
Anyway, I set the output baud rate to the same as the input baud rate and it seems to be behaving fine.
Now I just have to pull the sensor out of the exhaust tomorrow and calibrate it...
Thanks for the help, I'm sorry it was a stupid problem not at all related to what I thought it was...
Live and learn.

-Jeremy