Julien,
What is the Operating System on which your EMs and agents are running, respecitvely? In Windows environments, you can configure the system to prefer IPv4.
Additionally, in the [font=Courier New]IntroscopeEnterpriseManager.profile[font] of your EM configuration, setting the [font=Courier New]introscope.enterprisemanager.ipaddress[font] property to the IPv4 address of the EM host will make the EM only accept connections from agents or clients using IPv4, which might solve your problem. More information on this property is available in the
APM Bookshelf.
Finally, for your Java agents, you could also try adding the environment variable [font=Courier New]-Djava.net.preferIPv6Addresses=false[font] as one of the JVM's startup arguments.