At some point blizz got rid of the interface options to determine loot order and bag order. since then, if you had those options reversed on some characters, you had to run a command script to correct them. Since bagnon picks up the internal setting regarding loot order and then "reverses" it with the config options based on that, you end up with different chars behaving differently when the same options are checked. command scripts to fix loot order no longer work, or at least dont work in classic and TBC servers.

Proposed solution:
add a Profile screen where you can save your addon configurations to a certain profile. this would allow not only to specify for each char what config you want, but also to have different configs depending on playstyle. example one for farming, one for who knows

right now, if i log on with char A, i have items organized from top to bottom, left to right. settings are "Reverse bag/loot order" both checked. when i log with char B, i have items organized bottom to top, right to left. settings are still "Reverse bag/loot order" checked. whenever i switch characters i have to open config and check/uncheck those two options.