Are you using the USB to power the ShieldBuddy or the 9V power jack socket? If you have added a shield that draws too much current and you are using USB power, the red LED can come on or flash. Also if you are using USB power and you have a very cheap USB cable, these sometimes cannot pass enough current to run the ShieldBuddy.
If this happens it usually means that the USB power supply is not adequate or that the USB cable cannot pass enough current. If you have a shield that is powered off the ShieldBuddy then this can be a problem.