I've not ventured far enough into trapping in publisher (preferring to deal
with it in Trapwise).
but AFAIK trapping settings in nearly any application are honored only when
that application is creating the PostScript separations. That is, if one
goes to composite files you'll not get the overprints and such you'd expect.
This seems true in Quark and nearly anything else. (again, I've always tried
to deal with this issue in Trapwise)
If you are making a composite PDF I'd not exepct the overprints to stick.
BUT you can "repair" this using Pitstop Professional, an Acrobat plugin
that, unfortunatly, costs $500. If you do a lot of this, then it coould be
money well spent. If you don't....I have no solution. A demo is available at
enfocus.com, good for 30 days full functionality. Requires the full version
of Acrobat (not reader)