I just noticed this last night, and was able to verify that this is new to 4.2 beta 3.
I use shortcuts for some of my layouts, and since installing beta 3, I've noticed that when I use the "Update to current snapshot" option for a layout, it saves like it is supposed to but my shortcut still points to an older snapshot, instead of the one I just saved.
I can confirm that this is new to 4.2 beta 3 because I had saved a layout yesterday morning before going to work (using beta 2) and I'm able to retrieve that one just fine. After installing beta 3 last night, I've updated a few of my layouts & I can see that they've been saved if I look in the layouts menu, but the shortcut opens up the last saved layout before beta 3 was installed.
Can anyone else confirm this? For the programmers, I'd be happy to provide any additional information you may need, just let me know [:)]