I run Ice Dragon, sometimes sandboxed sometimes not.(I write "FireFox" a lot in this text below, imagine it says "Ice Dragon" )
What confuses me a bit is that I can make a setting in non-sandboxed ID, e.g. move my toolbar buttons around, and then if I open ID sandboxed I will have to make the same change there again.
What really confuses me though, is that when I quit the sandboxed Ice Dragon it will remember the changes I've made. surely if it's fully sandboxed it shouldn't do that..?
Once you run something in the sandbox for the first time it will take the information from the real system first then when you run it sandboxed again it will get the information from the previously sandboxed version of that application.
Lets make an example with FireFox, the first time you start FireFox in the sandbox it will use the settings you have on your current FireFox on your real system however from now on it will act like a completely different FireFox, if you close the sandboxed FireFox and then make changes to the "real" not sandboxed FireFox these changes won't move over to the Sandboxed FireFox since the next time you start FireFox in the sandbox it will gather the data from the instance of FireFox you had last time in the Sandbox.
In order to get the data from the unsandboxed instance of FireFox over to the sandboxed instance of FireFox you have to reset the Sandbox which means when you start FireFox in sandbox next time, it won't have any saved sandboxed data so it has to gather it from the real system again which is where the changes have been made to the unsandboxed FireFox.
This is the reason why Sandboxed FireFox remembers the changes you've made, because they are saved for the sandboxed FireFox but not for the FireFox that is not sandboxed. And as it is Fully Virtualized it is exactly what it should do, when you close the sandboxed FireFox it saves the data to the folder containing the sandbox data which is C:\VTRoot\ and when you start the sandboxed FireFox next time it will try to gather the information from there, though if no information exist it will take it from the real system which could
be something like C:\Programs and Files\FireFox\ or something like that.
Or did I misunderstand you and you mean that changes to the sandboxed FireFox is carried over to the non-sandboxed FireFox?