"Minutes Until Despawn After Inactive (0 = disabled)": 20,
this is how long the base remains on the map
"Minutes Until Despawn After Inactive Resets When Damaged": true,
this option can reset the timer for the above option
"Minutes Until Despawn After Looting (min: 1)": 45,
this option overrides both above options and is uninterruptable, and cannot be reset, once the base is looted or the TC is destroyed (if configured to end when TC is destroyed)
otherwise, no, i have no idea how your base is despawning before these times run out. the plugin cannot despawn the base when these conditions are not met, unless something is influencing this behavior and this cannot be fixed unless that influence is identified.
i have seen it happen myself a couple days ago, and now I recall a few instances of it supposedly happening before. my best guess is the server throws up a big F YOU sign and says no loot is left when there is. impossible? yes, but it's Rust, so...