If you crash out, the UI configuration will not save. That might be one reason it is not saved.
Also check your My Documents>My Games>FINAL FANTASY XIV>USER>*character code* folder. See if it is write protected or something preventing it being rewritten like bad sectors. Inside there should be a Log folder, a file named mcr0 (your macros) and ui (your... ui). See if they're missing and also check the date/time when it is last edited after you log out. If the time coincides then the game should be saving your UI if not... then spam the thread till someone else can help you