I have never used two serial ports operating at different baud rates, but I did notice that in the SoftwareSerial library examples, the code uses the "listen" function to explicitly select a port. Not sure if this would help, but I also came across another serial library while looking through forums of similar systems:
http://forum.arduino.cc/index.php?topic=54544.0
library link: NewSoftSerial | Arduiniana
May be capable of reading multiple baud rates. Seems to me it's something to do with the multiple serial connections because of this statement:
"Also, I just found out that if I turn off the main power to the system (powers RoboClaw logic plus the motors) and keep the Arduino connected to the USB (and hence powered up thru the USB), the Arduino program resumes normal operation and loop thru the while loop - strange.....)."
my theory: When the power source is disconnected from your roboclaw controller and you lose you serial connection, you no longer are getting conflicting serial messages, and your system works.
My overall suggestion would be to make an message pitch and catch between your serial connections and make sure you aren't crossing your messages within the code (and after loop iterations) before moving onto hardware, components, and wiring.