Nexus trapping is quite good. What trapping module are you using? Can you give a better example of whats not trapping. My guess is it's the settings, but not knowing more it's hard to guess.
I'm not sure what module I'm using (if you tell me how to check, I'll find out), but the scenarios where it let me down were very simple 2-color (Black plus Spot) situations where some things on the page trapped and others did not even though they obviously needed it. I've only been using it 2 months and it has happened on 3 different jobs. I've been doing this for over 17 years and there's nothing funky with these particular files that should give any trapping solution any problem.
Every RIP that I've seen that uses APPE has always had issues with flatting. RIP that uses Adobe Library and build there own can react much quicker then use adobe engine.
My own experience cannot back this up. Having used recent versions of both Prinergy and Apogee (both are APPE) over the past 4 years, I have not seen any flattening problems. In fact, my flattening problems disappeared with these RIPs.