@Mjth Welcome to the RobotShop Community. According to the manual:
The green LED marked Cells will blink the amount of cells you have attached when running in Lithium mode. Cells will also illuminate along with the Error LED if you have tripped the under-voltage alarm. The red Error LED illuminates if the Sabertooth has detected a problem. It will light if the driver has shut down due to a depleted battery or due to overheating, overcurrent or overvoltage. The Error LED will flash along with Cells if there is an issue with your battery. If both of those are blinking simultaneously, your battery is depleted.
Could it be your battery is in fact depleted?
Is your system somehow sending a signal to turn the motors, which are blocked from rotating?
A 6S LiPo should be fine (it can take 2S to 8S). Check the Lithium cutoff section of the guide (DIP 3).
Verify that your receiver is not receiving power from an external battery as well as the 5V BEC on the Sabertooth.