You should be delivering a CAD generated netlist which identifies
every pad on the board (top and bottom) and it's associated net name,
and xy location. In this way, if the gerber post processing does
something strange, it would be caught. You have to remember that gerber
artwork generation is a post process that is normally robust, but may
introduce errors. 
If a gerber extraction is done by the bareboard mfr., number 1 - it is
more expensive and 2) it will include these possible gerber errors.

Most bareboard mfrs can send you the format that this netlist file
should be in.

Tom Kavendek
Lucent Technologies
Murray Hill, N.J.