Is the pull-up resistor on SEN the one in the battery board, or is it an external pull-up? The battery board already has a pull-up on this line (all the lines connected to the DIP switch have one), so you do not really need it. You should not need to set your HOST_SOUT to high during initialization. As you are using the DIP switch to set SFLOW and PORTSEL to high, you do not really need to connect them to your MCU as well, unless you want to control the lines through software.
Are you driving the RESET pin for ANT from the RESET button on the battery board, or from an output on your MCU? Is it connected to the RESET pin at your MCU as well? Since some of the pins in your schematics are set by software rather than hardware (e.g. SFLOW, PORTSEL), they might be in an unknown state while your MCU is initializing, resulting in this odd behavior. If you intend to configure this lines by software, make sure that your MCU has been initialized and these lines are in a known state before you attempt to reset ANT.