I figured it out. The code was blinking one red and one green light, which means set/stops not set (which is a major fault and requires reprogramming them before it will return back to normal operation mode) Winnebago service manual does not supply you with programming manual for programming your in/out stops. I am assuming because they don't want you to damage the unit if you hold the buttons for too long. I downloaded the programming manual which you can access here http://support.powergearus.com/techdocs/3010001345.pdf
and reset the stops (manual is also attached below).
The only difference between my control unit and the one in the manual is that when moving in and out to set your stops, you must hold all 4 motor buttons on the top of the controller simultaneously while pressing the in/out to set your stops during the programming mode (that's the most difficult part). simply pressing the in/out button on the front of the control panel did not work.
Word of caution, make sure you are carefully watching your slide-out as you are setting the in/out functions or you may go too far damaging the siding or unit. if you wait too long (45 seconds) between programming both in or out, the unit will revert back to the trouble code and you will need to start all over again and wait for the unit to reset. If you did program it correctly the green and red lights will blink 3 times and then all lights will disappear. if you didnt do it correctly, both lights will blink very fast and you will need to wait a while (not sure how long) to do it again.
That just saved a $300 fee by the dealer to re-program stops!