Why does the APU Master Switch flash during a normal APU shutdown?
If it's the flap closing, you should be able to verify that from the APU ECAM page.

Based on the time frame you mentioned, most likely it's the simulated overspeed, which is part of the shutdown sequence and is basically the signal that closes the fuel solenoid (which you can also verify from the APU page).

APU flap closing comes later. For more on the shutdown sequence, see: Why would smoke enter the cabin if the batteries are switched off before the APU flap closes?


  The cool-down cycle lets the APU operate for 60 seconds at a low stabilized temperature. (...) Overspeed test occurs when the cool-down cycle is complete. The ECB supplies a signal to simulate an overspeed condition, that causes the fuel solenoid to close, and starts the APU shutdown. [emphasis added]


Source: APU training manual