When the TReX Jr starts up in either RC or analog mode, it first enters safe-start mode. In this mode, the three motors are shut down and are unaffected by the channel inputs. The TReX Jr lets you know its in this mode by rapidly flashing its green status LED. To exit this mode, the following conditions must all be simultaneously met:
If you have floating channels while running in analog mode, it may be impossible for you to satisfy the safe-start conditions. Bullet point #2 in the analog section (Section 4.d) provides several ways to fix this problem.
Once you have satisfied the safe-start conditions, the green status LED should stop flashing and turn solidly on. This indicates that the channel inputs are now in control of the motors.