So sending an 0x6, \n or \r didn't change anything. The usbserial still seems to crash the robot code one way or the other. I guess the next step is to track down a plain-ol-jane USB-Serial adapter and remove the arduino from the loop, just in case. I'll update again with more details.
On a secondary note, the MXP UART works just fine (which I suppose isn't surprising). After a little BrainDead(tm) moment we realized that RS232 is NOT compatible with Arduino UART (WHOOPS) which explains why that didn't work. I'm moderately surprised that we didn't murder the Arduino. I guess we were getting a little desperate & careless.
Edit:
Google managed to find this
http://www.chiefdelphi.com/forums/sh...d.php?t=136261
Which the forum search did not, somehow.
The post claims that the roboRio is documented to not be compatible with arduino, but I was unable to find said documentation. It also said the MXP port and DIO lines are 3.3v only, which scared me to death at first, but re-reading the RoboRio Manual All DIOs are 5V input compatible, so that's fine. I'm in the process of submitting a bug report to WPI.
I feel like this thread should be stickied or something, I've seen a _lot_ of people asking about serial ports and ardunios and such. It would probably be good so that people don't have to repeatedly go though the pain we have to understand the issues here.