let me shed some light on this...
all bags plugins use certain turbine API-s but turbine "ripped it off" as i saw in another post, so now every inventory / bag addon has the same problem.
This is exactly how the bug appears:
Say you have x equipped and want to equip y. You right click y, but instead of x going to bag, you see y moving to the position where x should have gone.
But actually y really is equipped and x really is in bag, you just don't see it right... bag is out of sync. One solution is to relog yes, but i prefer to unload, and reload.
Unfortunately unloading just a specific addon doesn't seem to work, so i unload all addons then reload them
Obviously i'm not tiping it all... I hahave an entire quickbar (hidden unless i press ctrl) with shortcuts for theese commands.
So this is what you need:
/shortcut 10 /plugins unload <unloads all plugins when clicked>
/shortcut 11 /plugins load FilterBag <reload fliterbag>
and each time you equip / unequip an item, click shortcut 10, then shortcut 11. this is a temporary hot-fix... turbine needs to fix they're own APIs.
This is the short of what i read, and a temporary solution... for more details,
here is a quote of goldbishop's from bellow: