The flashing(rotating) beacon is found on those units equipped with the K-9 APU(Auxiliary Power unit. This allows the main prime mover to shut down, while the secondary power unit will allow the air compessor to keep the train charged(as well allowing for lights and heat in the cab without any significant fuel consumption). CSX uses one system, while BNSF and NS and UP use a similar sistem referred to as "AESS"Automatic Engine Start System(or something to that effect). The prime mover can be started by a number of methods. If the yellow beacon was operating, that would indicate a fault of some kind with the K-9 APU system which in effect has rendered it inoperable, and would then have to be rest by the proper mechanical forces.
I know I'm getting old... My insurance company sent me only half a calendar this year!