Visually, it's an unpleasant mess but if we're going by item type and name, then it's very well organized. All of the duplicates/items/etc I plan on selling in the MP are on the very bottom, so whenever I happen to get a couple handful of new items, I will organize them to where they belong. Things go by rarity tier (MC, EI, Astra, CI, etc, gold shop, event, sponsor, game exchange, etc), then in alphabetical order within each subcategory, and then by year (only applies to holiday events). Been doing this type of organization in so long, I'm pretty used to it.
The inventory arranger doesn't mess up on me like many people are having though, so I assume it has to do with frequency of usage. My mules who hardly have as much items as my main (got like, 10+ pages of item equips alone). They (mule) glitches up every once in a while, which is very odd, but since I rarely go into their inventory arranger, it may take a while to enter the inventory database (maybe?). I could be wrong and am totally off the track with this odd glitch thing though. I remember from way back when that if you stay in the inventory arrange for too long, the saving process will mess up on you (similar to getting kicked out of Gaia due to lack of online activity).