Bit of a thread hijack, but on a similar note, I am trying to copy my macros.txt file across to another character (Save me setting up endless Spell Hotkey combinations) and it doesn't seem to pick up on the new character? Worked before for me >_< This character is on a different Shard, but I am navigating to the correct folder and copy/pasting accordingly...
To the OP, I have two characters called Izzy, first one I made has a Folder with the identical name, and the new character is under a folder called "Izzy2", each with there own customised files.
The only ways I know to force a Desktop save though, is logging out (and exiting the client?), or assigning the Save Desktop to a hotkey. The latter should definately work - when it does, you get displayed in the bottom right corner, "Desktop Saved.", confirming it's success.
If you're already trying one of the two and it's not working... then I'm at a loss -_-