Hello Vassilios,
just tried the par file you attached quickly, same problem, this time omitting (hence leaving them as "yes") the hdf5 options....same problem...is your hdf5 output regular?
I used current trunk of everything. I do get a plot that looks like the one you attach, which the one I would expect to see. There might be several reasons why we only see the coarsest level extent beyond the boundary some of which might be that VisIt just chops off the overlap (since it does try to remove the ghost zones). It's just artificial in any case and for a proper plot I'd add a clip to remove the negative extents and a reflect to produce a plot covering all quadrants anyway so I never worried about this. I would be more worried if I would still see the visible offset when going from one refinement level to the other but right now the data does not cross levels.
which version of visit do you use?
I used visit 2.4.2
this is using the latest trunk (checked out yesterday), but i am getting the same behaviour for ET_2012_11.
I have not tried the release version but think it should not differ since there were no changes to HDF5 that I am aware of since then.
Yours, Roland