Not sure what “External Net Missing” is… same with “Missing Copper” there’s a connection –it is defined in the Allegro database as a fill/pour.

[QUOTE]Not sure what “External Net Missing” is…  same with “Missing Copper” there’s a connection –it is defined in the Allegro database as a fill/pour… but it DRCs.  And I don’t see a way to turn this off. [/QUOTE]

External Net Missing means that at a certain location FAB 3000 has extracted a net (from your gerbers), but there is no reference about this in the IPC Netlist.  Usually this can be ignored because in most cases it may be a single point net with no connection (n/c).  If you wish to deactivate this check, then set the Netlist Compare options to be the following:
http://screencast.com/t/XwdvSx0qTiOl

Note: If you wish, to prevent FAB 3000 from generating Single Point Nets (during Netlist extraction) uncheck the option: "Allow Single Point Nets"
http://screencast.com/t/jf0ML1y0Y


Missing Copper is a bit more important.  This means the IPC file has defined a net to exist at a certain location, however when FAB 3000 queried over that coordinate there was not any copper found.  You mentioned there is a copper fill, perhaps if you could send me a sample workspace file (or screen capture of the area); I'll be happy to research further.