When that option is disabled, the backpack saves when the backpack is closed, if a change was made to the backpack while open.
In Backpacks v3.9, I silently removed that config option for performance and correctness. Now backpacks always save on server save. By saving when the server saves, if there is a server crash, the backpack data should basically be in sync with the world state, to avoid item loss or dupes. The usual issue with saving on server save is that many plugins save at that time, causing a lag spike when they all save. To avoid a lag spike, the plugin saves backpacks across multiple frames (one backpack per frame) so it can take up a few seconds to save all changed backpacks on a large server. For example, at 30 server fps, it would take 10 seconds to eventually save 300 backpacks (if that many backpacks had been modified since the previous server save). The exception is that if you unload the plugin, that causes all changed Backpacks to be saved instantly which may cause some lag if there was not a server save recently.
In Backpacks v3.9, even though backpacks are always saved on server save, they are no longer closed at that time, so you should no longer be seeing the above issue, though I might be missing something. If you are still using v3.8, please update to v3.9 and let me know if you are still seeing this issue.