I just upgraded to Assets 2.0 on EE 2.5.3. Installation went smoothly.
However my upload locations aren't acting correctly from within Assets.
My folder structure looks like this:
system html assets docs images minified themes
html/docs are both set up as upload directories in EE.
I'm using Master Config to set them. But even looking through the CP I can see they are correct. The server path is correct and the Upload Directory URL is absolute, not relative.
But the Assets file browser shows the folder structure of both directories as if they were pointed at the
html folder. (see screenshot)