[R-sig-Geo] polygons ignored rasterizing with R-raster rasterize()

[Jose Tanago]

Dear R-geo experts
I have experienced a weird problem rasterizing polygons with the
function "rasterize()" of Raster package.
Polygons that falls within the boundaries of another polygon are not
rasterized for an unknown reason. The output leave the inner pixels
(the ones overlaying the ignored polygons) without data

The ignored polygons are completely surrounded by another polygon but
the outer polygon do not spatially overlay (just enclosed). All the
polygons were created by segmenting a raster with the same pixel size
and exactly equal spatial structure. So, the concerned empty pixels
centers are perfectly covered by the inner polygon (the one ignored),
while the outer polygon do not cover at all the concerned pixels.

Do you have any idea what is wrong and how to overcome it?
(I have rasterized the same vector with ARGIS and those polygons
ignored in rasterize() are well rasterized by the ARCGIS tool)
thanks in advance for any hint.
Best
Jose