We currently have version 1.58 of Inv tweaks installed on our server, unfortunately this is preventing us from using any kind of chest or GUI plugin as inventory tweaks will resort predesigned shops/gui's using the sorting functions. It only takes 1 player to do this and the shop/gui will be messed up for everyone on the server.

The servers InvTweaks.cfg file is having no effect on the server what-so-ever.

This makes this mod a pretty bad grief/exploit mod.

Could I request that server side configs be given priority (and work as intended)

Server-side mode has no config, it is designed specifically to bypass vanilla inventory handling (and all bukkit/etc. plugins) to fix a bug typically experienced with modded items.