I recently came across a bug in the e-transmit routine that you might be interested in.
It occurs when on of the drawings you want to send (e.g. A.dwg) is xref'ed into another (e.g. B.dwg) and you try etransmit both at the same time. You will get a warning that A.dwg is already part of the package, so the routine will not add it again. At this point, A.dwg has any overlayed xrefs of its own, they will not be included in the package because B.dwg doesn't see them.
The best solution that i know of is to go back and etransmit A.dwg the file individually.
Brian