In my experience, job gauges are by far the most common UI element to randomly reset to their default position/display mode. I've also noticed it happen with the item selection window for quest turn-ins, as well as the Eureka/Bozja duty UIs, albeit rarely.

The one workaround I found for this issue is to keep a copy of the currently active HUD layout as a backup. Whenever the UI elements reset, they only reset in the active layout, so restoring them to their modified position/display mode is as simple as copying the backup HUD layout into the active layout (e.g. copy layout 4 into layout 1).