Reproduced with Inkscape 0.48.1 and 0.48+devel r10129 on OS X 10.5.8, both using the command line or the GUI option.
The export limited to an id seems to ignore or miscalculate the transform of the parent group(s) e.g. of the top-level layer after resizing the page.
Attached modified version works for me: the three groups have been moved onto a new layer (which doesn't have an explicit 'transform' attribute when created after resizing the page) and the exported PDF/EPS fully includes the group with the id 'missing'.
Reproduced with Inkscape 0.48.1 and 0.48+devel r10129 on OS X 10.5.8, both using the command line or the GUI option.
The export limited to an id seems to ignore or miscalculate the transform of the parent group(s) e.g. of the top-level layer after resizing the page.
Attached modified version works for me: the three groups have been moved onto a new layer (which doesn't have an explicit 'transform' attribute when created after resizing the page) and the exported PDF/EPS fully includes the group with the id 'missing'.