I had this problem too. The solution for me was, that the layout I was choosing had an extra bar on top. But the frames I was copying it to hadn't this module enabled. Enabling that module allowed the frames to retain the layout. So the fix is, when a layout is copied it should enable disabled modules that are used for that layout.... Ugh hope that made sense.
Here's another reference to an answer describing what I mean:
Thanks for pointing me in the right direction. Here is what I found. The UFs I made have a blank space in them (Health bar|Blank Space|Power Bar). When I created each UF I made the Player Frame first then all the other frames were copied from the player frame. I enabled the blank space for each UF. Next I began customizing all the different texts (Health etc.). After customizing the text for the Player Frame I went to all the other frames and used other----->layout----->copy from other frame and selected player. For some reason when you copy another frame it will disable the blank space, although the blank space doesn't disappear until you log out or /reloadui. After log out or /reloadui if you go to the frames missing the blank space and re-enable it the frames work fine and are saved between log outs.