Well Scott,
I could say that I'm handling with lot of bundles from lot of Eclipse projects in my Tycho buildings since a year and the only problem that I had until now was with sources from ECF.
I have to exclude such sources bundles from the source feature configuration to make the build go:
<build>
<plugins>
<plugin>
<groupId>org.eclipse.tycho.extras</groupId>
<artifactId>tycho-source-feature-plugin</artifactId>
<version>${tycho-version}</version>
<executions>
<execution>
<id>source-feature</id>
<phase>package</phase>
<goals>
<goal>source-feature</goal>
</goals>
</execution>
</executions>
<configuration>
<labelSuffix> (source)</labelSuffix>
<excludes>
<plugin id="org.eclipse.ecf.presence" />
<plugin id="org.eclipse.ecf.provider.irc" />
<plugin id="org.eclipse.ecf.provider.bittorrent" />
<plugin id="org.eclipse.ecf.provider.msn" />
<plugin id="org.eclipse.ecf.presence.bot" />
<plugin id="org.eclipse.ecf.telephony.call" />
<plugin id="org.eclipse.ecf.protocol.msn" />
<plugin id="org.eclipse.ecf.provider.filetransfer.efs" />
<plugin id="org.eclipse.ecf.docshare" />
<plugin id="org.eclipse.ecf.provider.filetransfer.scp" />
<plugin id="org.eclipse.ecf.remoteservice.ui" />
<plugin id="org.eclipse.ecf.protocol.bittorrent" />
<plugin id="org.eclipse.ecf.sync" />
<plugin id="org.eclipse.ecf.storage" />
<feature id="org.eclipse.ecf.xmpp.feature" />
<feature id="org.eclipse.ecf.discovery.feature" />
<feature id="org.eclipse.ecf.datashare.feature" />
<feature id="org.eclipse.ecf.discovery.zookeeper.feature" />
<feature id="org.eclipse.ecf.discovery.dnssd.feature" />
<feature id="org.eclipse.ecf.discovery.jmdns.feature" />
<feature id="org.eclipse.ecf.discovery.slp.feature" />
<feature id="org.eclipse.ecf.osgi.services.feature" />
<feature id="org.eclipse.ecf.server.generic.feature" />
<feature id="org.eclipse.ecf.remoteservice.feature" />
<feature id="org.eclipse.ecf.remoteservice.soap.feature" />
<feature id="org.eclipse.ecf.remoteservice.rest.feature" />
<feature id="org.eclipse.ecf.remoteservice.rosgi.feature" />
<feature id="org.eclipse.ecf.xmpp.feature" />
</excludes>
</configuration>
</plugin>
I'll investigate a bit more the bundle contents to try to identify the problem.