My main character is a happy camper. Everything is running smoothly there. Whenever I log on to another character though all the bag slots are reversed in such a way that using reverse bag order or reverse slots does not fix it without leaving gaps.

All settings are the same throughout the characters but its still just my main one that the addon works properly for. The primary bag that you always have is on top if I don't reverse any orders in the settings, yet it still sorts things from the last bag and backwards. Picture for clarification.

Ok, things just got even weirder. This is my bags after clicking to clean up bags.

I have noticed for quite some time now that, if it's a "Boosted" character bagnon doesn't seem to like the sorting, like.. at all. It throws things all over the bag, I have to hit reverse bag order or reverse sort order to get it to do anything. When I do, I have to go back in and re adjust it though, a lot.

If it's a normally leveled character there's no problems. It starts at the top and works to the bottom like it should. But every single one of my boosted characters (from purchasing expansion packs) gets screwed up. Even if I uninstall the addon and clear out my cache/wtf folders etc. As soon as I re install the addon it does the same thing, to the same exact characters.
It also affects characters that realm transfer for some reason.
Normal characters that have been on the same server and leveled regularly though are totally unaffected.

I'm having the same problem! Any update on what's causing this to happen? Not having clean bags really annoys me!

I'm having the same problem on just one character! My character realm transferred so as @NoxElohim stated it affects them too. Hopefully you'll be able to fix it soon, it's really really annoying