I've been experiencing this behavior off-and-on for years now, and hilariously enough, am finally getting around to asking the public for answers:
1) When I log into my account, the order of my frame/armour's slots are reversed. For instance, I prefer having my V101, Adept, and V801 taking up the bottom three so that the top one is my spare and is quickly interchangeable during gameplay (cures,v502, etc.). This becomes annoying when the V101 ends up on top, which I would never swap for anything...
2) Once I re-order the slots to my liking, they stay that way, so long as I remain logged in.
3) This doesn't happen 100% of the time, but lately it has seemed like it.
For all you visual learners out there, Here's a screenshot