I am guessing on this one but I would first ask if you calibrated the speed controllers. The calibration procedure sets the maximum speed forward and reverse as sent by the joysticks. In "auto mode" you were likely sending a higher value to the speed controllers than in joystick/human mode. This is a simple fix.
As to the chippies (I prefer "chalupa" myself.) these motors are designed to give max output power at a very high RPM, so if you want to get the max out of the motor, you have to design your gear ratios appropriately. This is not something to guess at and the size of you tires makes a big difference in the design. Choose a gear ratio that is too low and you will stall, too high and you will not run fast but you will have lot's of power. Joe Johnson and many others have spent a lot of time writing about this subject, see the White papers section on this site.
http://www.chiefdelphi.com/forums/pa...C&pagenumber=3