In both cases 2 & 3 it appears the repeater was programmed to do this. Normally you would implement your own repeater code to your specifications. I am not really sure what the repeater is set up to do. I am going to forward this to someone else who might have more comments to add.
BTW: You must make sure the repeater code has stopped running before running scripts or modifying bits. The repeater code can and will go back in and change the registers to what it wants. Repeater code and scripts are some what mutually exclusive.