When you update the firmware a popup lists all the changes for the current firwmare. To be safe I recommend resetting your settings to default if you are having problems and re-setup everything setup by step. Let me know if you still have problems and what they are.
Roboclaw firmware changes from 4.1.27 to 4.1.29:
//Removed test code that was interfering with user selected current limit
//Reduced overhead when using exponential option in RC/Analog
//Added Serial communications timeout Motor Safe Stop option
//Added current blanking adjustment(0% to 20% blanking period, default 5.3%, Sign Magntiude mode only)
//Added Main and Logic battery Offsets(+-1v range)
//Added Velocity and Position error limits
//Added back calculation for speed and position variables for smooth transitions from PWM to Speed to Position control modes while motors are active.
//All errors, except E-Stop, now freewheel motors(disable mosfet drivers). E-Stop still brakes motors.
//Over voltage freewheels motors until voltage drops back under Maximum voltage limit(previously motors would hard brake until the voltage dropped).
//Fixed mixed encoders types conflict on 2x7A models(other models were not affected).