The ext light flashes if any routed input is unlocked, whether that input is being used or not. It could be argued (and often is) that the "or not" part is foolish, but it's difficult …
The mysteriousness of your issue is probably due to an input being on the edge of locking. If you check the lock states of all inputs, and either fix the unlocked ones, or unroute unused ones, the flashing will go away. Note that "inputs" also includes direct connections to outputs.
