I had this exact same issue. I was able to enable Territory War, TW timer settings, etc by making changes to the server file located at
/PWServer/155/gdeliveryd/gamesys.conf
(If you're not running 155, just use the version that you are using in place of the 155 [i.e.136, etc])
Under the [GDeliveryServer] section:
Ensure that the following are set as 1. (By default, 343's releases have both PvP and countrybattle (TW) disabled.)
countrybattle = 1
Here is the setting that enables the TW Timer function to trigger the TW start announcements, enables the NPC quest at the teleporters, etc.
battle_time_mode=1
Also, be sure that this setting is set to 1 under:
[COUNTRYBATTLE]
is_countrybattle_open=1
I hope this helps anyone else configuring their server, as I spent a significant number of hours searching this forum, interwebs, tracking this down and testing on my personal test server, etc.
-SciTech