If it's fast red blink (about 5 times per second), that simply means the jaguar is powering the motor backwards. If it's a slower blink (around 2 times per second..ish) that means a fault condition which is:
Under voltage (check battery)
Over Temperature (Turn off robot for a few minutes)
Over Current (Make sure motors aren't stalling)
Limit Switch (Make sure jumpers are in if you're not using limit switches; make sure your limit switches are normally closed if you are)
If you are using the CAN bus, you can figure out which one it is programatically.
See
here for more information about the jaguars.
However, a red blinking light (either fast or slow) means that the code is doing something.