Steve,
After generating a platform XML for each NEM and running an emane process in 
each container, I still had the same problem with all packets being received 
(with no log messages from the mac/phy layers.)

My new platform and NEM XML looked like this:

<platform>
  <param name="otamanagerchannelenable" value="on"/>
  <param name="otamanagergroup" value="224.1.2.8:45702"/>
  <param name="otamanagerdevice" value="ctrl0"/>
  <param name="eventservicegroup" value="224.1.2.8:45703"/>
  <param name="eventservicedevice" value="lo"/>
  <param name="controlportendpoint" value="0.0.0.0:47000"/>
  <param name="antennaprofilemanifesturi" value=""/>
  <nem definition="n4emane_rfpipenem.xml" id="1" name="tap1.0.155">
    <transport definition="n4transvirtual.xml" group="1">
      <param name="device" value="eth0"/>
    </transport>
  </nem>
</platform>

<nem name="RF-PIPE NEM">
  <mac definition="n4emane_rfpipemac.xml"/>
  <phy definition="n4emane_rfpipephy.xml"/>
</nem>

Working through the EMANE tutorials I found that even though I had a transport 
tag defined for each NEM (in the platform XML), the NEM XML itself also needed 
the transport tag:

<nem name="RF-PIPE NEM">
  <transport definition="n4transvirtual.xml"/>
  <mac definition="n4emane_rfpipemac.xml"/>
  <phy definition="n4emane_rfpipephy.xml"/>
</nem>

This is described in your 0.9.2 release notes: "The new platform.dtd and 
nem.dtd require transport elements to be at the top of the layer stack."

When working properly the emane log looks like this:
13:48:55.225307  INFO TRANSPORTI 001 VirtualTransport::configure bitrate: 0
...
13:48:55.225887  INFO MACI 001 RFPipeMACLayer::configure datarate = 1000000
...
13:48:55.226111  INFO PHYI 001 FrameworkPHY::configure: bandwidth = 1000000 Hz

And when it was broken:
12:14:38.824917  INFO MACI 001 RFPipeMACLayer::configure datarate = 1000000
...
12:14:38.825223  INFO PHYI 001 FrameworkPHY::configure: bandwidth = 1000000 Hz
...
12:14:38.826302  INFO TRANSPORTI 001 VirtualTransport::configure bitrate: 0

It was strange that not having the transport definition at the top passed the 
XML validation and produced an environment where everything seemed connected 
(when the mac/phy layers really were being bypassed.) I guess the XML 
flexibility allows for the external vs internal transport.

-Jeff
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