I started creating a GUIDE GUI in 2014a and have just upgraded to 2014b. I was aware that some GUI elements may be hidden due to the new graphics system. And, lo and behold, parts were "missing" when I ran it. I fixed these minor points and carried on.
However, larger parts of the GUI, which initially worked in 2014b, disappeared (as well as having the positions of some elements reset to [0,0,1,1]). So, with a big pot of coffee, away I went fixing it, moving things back and front and in and out of their parent panels. Then I re-ran my and GUI everything looks as it should.
The catch, however, is when I close and re-run GUIDE (after saving), big chunks of the GUI are not visible in GUIDE. When I run the GUI, however, everything is as it should be. I have re-tweak the GUI in GUIDE to make elements visible, and it all works fine. But again, saving and restarting GUIDE leaves elements hidden. The GUI, however, still looks as it should.
In short, my GUI works as it should, but it is a pain to edit with GUIDE because of the elements being hidden. This is my first GUI, so missing something really obvious is a possibility. I'm running 2014b, on OS X Mavericks.