> I can also reproduce with libtiff 3.9.2. libtiff 3.X suffers sometimes from
> some problems when generating overviews in a interleaved way, as it is
> done by BuildOverviews("NEAREST", [2,4,8,16]). Those problems have been
> corrected in libtiff 4.0
> 
> A way to workaround this is to generate each overview level one after
> another one, like this :
> 
> out_ds.BuildOverviews("NEAREST", [ 2 ])
> out_ds.BuildOverviews("NEAREST", [ 4 ])
> out_ds.BuildOverviews("NEAREST", [ 8 ])
> out_ds.BuildOverviews("NEAREST", [ 16 ])
> 
> This will work on both libtiff 3.X and libtiff 4.0. Note that it might
> perform a little less than generating all the levels in a single
> instruction, since the source data must be read several times.

In the libtiff 3.X case, I've just implemented in GDAL trunk the workaround in 
the GTiff driver
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